Merge branch 'main-rc' into b3.1.4

RELEASE.txt

@@ -1,353 +1,72 @@
-SLS Detector Package 3.1.0 released on 2018-03-12
+SLS Detector Package 3.1.4 released on 2018-08-17
 =================================================
 
 
 
 INTRODUCTION
 
-This document describes the differences between 3.1.0 and 3.0.0 releases.
+This document describes the differences between 3.1.4 into 3.1.3 releases.
 
-The conda package of the binaries can be downloaded from
-	
-	https://github.com/slsdetectorgroup/sls_detector_software.git
-	
-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
-	
-	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
-	
-User documentation can also be accessed directly at this location:
-
-    https://www.psi.ch/detectors/users-support
-
-If you have any software related questions or comments, please send them to:
-
-    dhanya.thattil@psi.ch
-    anna.bergamaschi@psi.ch
-    
-If you have any python related questions or comments, please send them to:
-	
-	erik.frojdh@psi.ch
-
-
-CONTENTS
-
-- Firmware Requirements
-- Changes in User Interface
-- New Features
-- Resolved Issues
-- Known Issues
-
-
-
-Firmware Requirements
-=====================
-
-	Please refer to the link below for more details on the firmware versions.
-		https://www.psi.ch/detectors/firmware.
-
-    	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              : 20
-        
-    	-Can be upgraded remotely via bit files.
-    
-        
-    	Jungfrau
-    	========       
-    	Minimum compatible version  : 13.11.2017
-    	Latest version              : 13.11.2017
-
-    	-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 for firmware dated 08.02.2018 and 09.02.2018 
-		(25 um Slave) 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
-	---
-	19.	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.
 
+Topics Concerning
+==================
+	- get settings in users class
+	- HDF5 in Receiver
+	- gotthard timer accuracy
 
 
 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.
+	1.	Users class setSettings(-1) gave undefined settings. Has been fixed.
 	
-	2. 	Updated writing content of config and parameter dump into files.
+	2. 	Users class timers give more precise values now.
 	
-	3. 	More locking to handle main and processing threads using the threadpool.
-		Removing unlock twice, which is undefined behavior.
-		
-	4.	(Jungfrau) adcphase returns the correct value, instead of -1.
+	3.	When deleting slsDetector object, Stop socket deletion includes a close on 
+		default file descriptor zero (which it didn't open, just set for flag).
+		This is fixed with temporary solution, to connect stop socket at checkOnline
+		to set file descriptor to the right one. Later releases will use exception
+		to handle constructor error flags.
 
 	
 	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.
+	1.	(Gotthard) Timers converted from time in nanoseconds to number of cycles
+		is made more precise now. Clock value changed from 32.1E+6 to 32.007729E+6. 
 	
 	
 	Receiver
 	--------	
-	12.	Made it easier to disable the standard receiver and fixing bugs related 
-		to the use of a custom one. 
+	1.	Jungfrau Single Module Master files did not link to the HDF5 data file properly.
+		This is fixed now.
 		
-	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.
+	2.	Relative linking is used in the HDF5, instead of absolute now.
 	
 
 
-Known Issues
+New Features
 ============
 
-
 	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).
-
+	1.	Timers can be set/retrieved individually. It has been introduced because
+		Gotthard 25um can have different delays for master and slave modules.
 
 	Receiver
 	--------
-	3. 	HDF5 compression and filters are not implemented yet.
-	
-
-	
-
+	1.	HDF5 x dimension (#images). Max made unlimited. Chunked Dataset by default.
+		
+		When receiver gets an image more than #frames, the HDF5 dataset will 
+		extend itself in the x dimension by another #frames. So, one can do
+		(in Jungfrau, Gotthard, NOT Eiger)
+		sls_detector_put resetframescaught 0
+		sls_detector_put receiver start
+		sls_detector_put status start
+		sls_detector_put status start
+		...
+		sls_detector_put receiver stop
 		
 	
 		

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manual/docs/html/slsDetectorClientDocs/config.html

@@ -183,7 +183,7 @@ Versions</a></h2>
 Speed</a></h2>
 <p>commands to configure speed of detector</p>
 <ul>
-<li><b>clkdivider [i]</b> sets/gets the readout clock divider. EIGER, JUNGFRAU [0(fast speed), 1(half speed), 2(quarter speed)]. MYTHEN[???]. <code>Returns</code> <code></code>(int)</li>
+<li><b>clkdivider [i]</b> sets/gets the readout clock divider. EIGER, JUNGFRAU [0(fast speed), 1(half speed), 2(quarter speed)]. Jungfrau, full speed is not implemented and overwrites adcphase to recommended default. MYTHEN[???]. <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
 <li><b>setlength [i]</b> sets/gets length of set/reset signals (in clock cycles). Used in MYTHEN only. <code>Returns</code> <code></code>(int)</li>
@@ -207,7 +207,7 @@ Speed</a></h2>
 <li><b>adcclk [i]</b> sets/gets the ADC clock frequency in MHz. For the new chiptestboard!<code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
-<li><b>adcphase [i]</b> Sets/gets the ADC clock frequency in MHz. For the new chiptestboard!<code>Returns</code> <code></code>(int)</li>
+<li><b>adcphase [i]</b> Sets/gets phase of the sampling clock. For JUNGFRAU, setting speed (clkdivider) overwrites adcphase to its default recommended value. (Not for EIGER) <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
 <li><b>adcpipeline [i]</b> Sets/gets the pipeline of the ADC. For the new chiptestbaord!<code>Returns</code> <code></code>(int)</li>
@@ -251,7 +251,7 @@ Detector Parameters</a></h2>
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manual/docs/html/slsDetectorClientDocs/settings.html

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manual/docs/html/slsDetectorClientHowTo/index.html

@@ -43,7 +43,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <H1 ALIGN="CENTER">SLS Detector text clients manual</H1>
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-<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 20, 2018</STRONG></P>
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@@ -148,7 +148,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-03-20
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorClientHowTo/node1.html

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 Thattil Dhanya
-2018-03-12
+2018-03-20
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manual/docs/html/slsDetectorClientHowTo/node2.html

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 Thattil Dhanya
-2018-03-12
+2018-03-20
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manual/docs/html/slsDetectorClientHowTo/node3.html

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 Thattil Dhanya
-2018-03-12
+2018-03-20
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manual/docs/html/slsDetectorClientHowTo/node4.html

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 Thattil Dhanya
-2018-03-12
+2018-03-20
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 </HTML>

manual/docs/html/slsDetectorClientHowTo/node5.html

@@ -160,7 +160,7 @@ sls_detector_put ratecorr -1
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-03-20
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorClientHowTo/node6.html

@@ -61,11 +61,11 @@ Mathematics Department, Macquarie University, Sydney.
 The command line arguments were: <BR>
  <STRONG>latex2html</STRONG> <TT>-split 4 slsDetectorClientHowTo.tex</TT>
 <P>
-The translation was initiated by Thattil Dhanya on 2018-03-12
+The translation was initiated by Thattil Dhanya on 2018-03-20
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-03-20
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorClientHowTo/slsDetectorClientHowTo.html

@@ -43,7 +43,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <H1 ALIGN="CENTER">SLS Detector text clients manual</H1>
 <DIV>
 
-<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 20, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -148,7 +148,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-03-20
 </ADDRESS>
 </BODY>
 </HTML>

manual/manual-api/mainClient.cpp

@@ -71,11 +71,6 @@ int main(int argc,  char **argv) {
 
 	/** - registering data callback */
 	pDetector->registerDataCallback(&dataCallback, NULL);
-	/** - if receiver exists, enable data streaming from receiver to get the data */
-	pDetector->enableDataStreamingFromReceiver(1);
-	/** - create zmq sockets in client to enable data streaming in of data from receiver/different process */
-	pDetector->enableDataStreamingToClient(1);
-
 
 
 	/** - ensuring detector status is idle before starting acquisition. exiting if not idle */

serverBin/eigerDetectorServerv3.1.0.16.1

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

serverBin/eigerDetectorServerv3.1.1.16.0

@@ -0,0 +1 @@
+../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServerv3.1.1.16.0

serverBin/gotthardDetectorServerv3.1.0.1

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

serverBin/gotthardDetectorServerv3.1.4.0

@@ -0,0 +1 @@
+../slsDetectorSoftware/gotthardDetectorServer/gotthardDetectorServerv3.1.4.0

serverBin/jungfrauDetectorServerv3.1.0.2

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

serverBin/jungfrauDetectorServerv3.1.3.0

@@ -0,0 +1 @@
+../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServerv3.1.3.0

slsDetectorGui/gitInfo.txt

@@ -1,9 +1,9 @@
 Path: slsDetectorsPackage/slsDetectorGui 
 URL: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
 Repository Root: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
-Repsitory UUID: b389402d647e939342dbb2c9317c688c0eb6b105 
-Revision: 452 
-Branch: 3.1.0-rc 
-Last Changed Author: Erik_Frojdh 
-Last Changed Rev: 3458 
-Last Changed Date: 2018-03-09 10:55:40.000000002 +0100 ./src/qTabSettings.cpp
+Repsitory UUID: 1b92b01a466aa1986b8198700274af75477a1e54 
+Revision: 455 
+Branch: 3.1.4 
+Last Changed Author: Dhanya_Thattil 
+Last Changed Rev: 3492 
+Last Changed Date: 2018-08-17 16:36:24.000000002 +0200 ./src/qTabSettings.cpp

slsDetectorGui/include/gitInfoGui.h

@@ -1,6 +1,6 @@
 #define GITURL "git@github.com:slsdetectorgroup/slsDetectorPackage.git"
-#define GITREPUUID "b389402d647e939342dbb2c9317c688c0eb6b105"
-#define GITAUTH "Erik_Frojdh"
-#define GITREV 0x3458
-#define GITDATE 0x20180309
-#define GITBRANCH "3.1.0-rc"
+#define GITREPUUID "1b92b01a466aa1986b8198700274af75477a1e54"
+#define GITAUTH "Dhanya_Thattil"
+#define GITREV 0x3492
+#define GITDATE 0x20180817
+#define GITBRANCH "3.1.4"

slsDetectorSoftware/eigerDetectorServer/gitInfo.txt

@@ -1,9 +1,9 @@
 Path: slsDetectorsPackage/slsDetectorSoftware/eigerDetectorServer 
 URL: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
 Repository Root: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
-Repsitory UUID: 8b02aa9e91bbee0470492dcf1ff67415851e14fa 
-Revision: 315 
-Branch: 3.1.0-rc 
-Last Changed Author: Erik_Frojdh 
-Last Changed Rev: 3455 
-Last Changed Date: 2018-03-08 16:44:32.000000002 +0100 ./FebRegisterDefs.h
+Repsitory UUID: afac5be3c3674fe87044d3b7a54471291698d4ba 
+Revision: 316 
+Branch: 3.1.1-rc 
+Last Changed Author: Dhanya_Thattil 
+Last Changed Rev: 3467 
+Last Changed Date: 2018-03-19 17:26:38.000000002 +0100 ./FebRegisterDefs.h

slsDetectorSoftware/eigerDetectorServer/gitInfoEiger.h

@@ -1,6 +1,6 @@
 #define GITURL "git@github.com:slsdetectorgroup/slsDetectorPackage.git"
-#define GITREPUUID "8b02aa9e91bbee0470492dcf1ff67415851e14fa"
-#define GITAUTH "Erik_Frojdh"
-#define GITREV 0x3455
-#define GITDATE 0x20180308
-#define GITBRANCH "3.1.0-rc"
+#define GITREPUUID "afac5be3c3674fe87044d3b7a54471291698d4ba"
+#define GITAUTH "Dhanya_Thattil"
+#define GITREV 0x3467
+#define GITDATE 0x20180319
+#define GITBRANCH "3.1.1-rc"

slsDetectorSoftware/gitInfo.txt

@@ -1,9 +1,9 @@
 Path: slsDetectorsPackage/slsDetectorSoftware 
 URL: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
 Repository Root: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
-Repsitory UUID: b389402d647e939342dbb2c9317c688c0eb6b105 
-Revision: 1714 
-Branch: 3.1.0-rc 
-Last Changed Author: Erik_Frojdh 
-Last Changed Rev: 3458 
-Last Changed Date: 2018-03-12 14:19:44.000000002 +0100 ./threadFiles/ThreadPool.o
+Repsitory UUID: 1b92b01a466aa1986b8198700274af75477a1e54 
+Revision: 1726 
+Branch: 3.1.4 
+Last Changed Author: Dhanya_Thattil 
+Last Changed Rev: 3492 
+Last Changed Date: 2018-08-17 17:57:11.000000002 +0200 ./threadFiles/ThreadPool.o

slsDetectorSoftware/gotthardDetectorServer/firmware_funcs.c

@@ -906,20 +906,15 @@ int64_t getFrames(){
 int64_t setExposureTime(int64_t value){
   /* time is in ns */
   if (value != -1) {
-	  double actualvalue = value*(1E-9*CLK_FREQ);
-	  value*=(1E-9*CLK_FREQ);
-	  if(fabs(actualvalue-value)>= 0.5){
-	    if(actualvalue > value)
-	      value++;
-	    else
-	      value--;
+	  value = (value * 1E-3 * CLK_FREQ ) + 0.5;
   }
-  }
-    return set64BitReg(value,SET_EXPTIME_LSB_REG, SET_EXPTIME_MSB_REG)/(1E-9*CLK_FREQ);
+    return (set64BitReg(value,SET_EXPTIME_LSB_REG, SET_EXPTIME_MSB_REG) /
+    		(1E-3 * CLK_FREQ)) + 0.5;
 }
 
 int64_t getExposureTime(){
-  return get64BitReg(GET_EXPTIME_LSB_REG, GET_EXPTIME_MSB_REG)/(1E-9*CLK_FREQ);
+  return (get64BitReg(GET_EXPTIME_LSB_REG, GET_EXPTIME_MSB_REG) /
+		  (1E-3 * CLK_FREQ)) + 0.5;
 }
 
 int64_t setGates(int64_t value){
@@ -933,23 +928,16 @@ int64_t getGates(){
 int64_t setPeriod(int64_t value){
   /* time is in ns */
   if (value!=-1) {
-	  double actualvalue = value*(1E-9*CLK_FREQ);
-	  value*=(1E-9*CLK_FREQ);
-	  if(fabs(actualvalue-value)>= 0.5){
-	    if(actualvalue > value)
-	      value++;
-	    else
-	      value--;
-	  }
+	  value = (value * 1E-3 * CLK_FREQ ) + 0.5;
   }
 
-
-
-  return set64BitReg(value,SET_PERIOD_LSB_REG, SET_PERIOD_MSB_REG)/(1E-9*CLK_FREQ);
+  return (set64BitReg(value,SET_PERIOD_LSB_REG, SET_PERIOD_MSB_REG) /
+		  (1E-3 * CLK_FREQ)) + 0.5;
 }
 
 int64_t getPeriod(){
-  return get64BitReg(GET_PERIOD_LSB_REG, GET_PERIOD_MSB_REG)/(1E-9*CLK_FREQ);
+  return (get64BitReg(GET_PERIOD_LSB_REG, GET_PERIOD_MSB_REG) /
+		  (1E-3 * CLK_FREQ)) + 0.5;
 }
 
 int64_t setDelay(int64_t value){
@@ -959,16 +947,11 @@ int64_t setDelay(int64_t value){
 		  value += masterdefaultdelay;
 		  cprintf(BLUE,"Actual delay for master: %lld\n", (long long int) value);
 	  }
-	  double actualvalue = value*(1E-9*CLK_FREQ);
-	  value*=(1E-9*CLK_FREQ);
-	  if(fabs(actualvalue-value)>= 0.5){
-	    if(actualvalue > value)
-	      value++;
-	    else
-	      value--;
+	  value = (value * 1E-3 * CLK_FREQ ) + 0.5;
   }
-  }
-  int64_t retval = set64BitReg(value,SET_DELAY_LSB_REG, SET_DELAY_MSB_REG)/(1E-9*CLK_FREQ);
+
+  int64_t retval = (set64BitReg(value,SET_DELAY_LSB_REG, SET_DELAY_MSB_REG) /
+		  (1E-3 * CLK_FREQ)) + 0.5;
   if (masterflags == IS_MASTER) {
 	  cprintf(BLUE,"Actual delay read from master: %lld\n", (long long int) retval);
 	  retval -= masterdefaultdelay;
@@ -978,7 +961,8 @@ int64_t setDelay(int64_t value){
 }
 
 int64_t getDelay(){
-  return get64BitReg(GET_DELAY_LSB_REG, GET_DELAY_MSB_REG)/(1E-9*CLK_FREQ);
+  return (get64BitReg(GET_DELAY_LSB_REG, GET_DELAY_MSB_REG) /
+		  (1E-3 * CLK_FREQ)) + 0.5;
 }
 
 int64_t setTrains(int64_t value){
@@ -996,37 +980,26 @@ int64_t setProbes(int64_t value){
 
 
 int64_t setProgress() {
-
   //????? eventually call after setting the registers
-
 return 0;
 
 }
 
 
 int64_t getProgress() {
-
-
   //should be done in firmware!!!!
-
 	return 0;
 
 }
 
 int64_t getActualTime(){
-  return get64BitReg(GET_ACTUAL_TIME_LSB_REG, GET_ACTUAL_TIME_MSB_REG)/(1E-9*CLK_FREQ);
+  return (get64BitReg(GET_ACTUAL_TIME_LSB_REG, GET_ACTUAL_TIME_MSB_REG) /
+		  (1E-3 * CLK_FREQ)) + 0.5;
 }
 
 int64_t getMeasurementTime(){
   int64_t v=get64BitReg(GET_MEASUREMENT_TIME_LSB_REG, GET_MEASUREMENT_TIME_MSB_REG);
- /* u_int64_t mask=0x8000000000000000;
-  if (v & mask ) {
-#ifdef VERBOSE
-    printf("no measurement time left\n");
-#endif
-    return -1E+9;
-  } else*/
-    return v/(1E-9*CLK_FREQ);
+    return (v / (1E-3 * CLK_FREQ)) + 0.5;
 }
 
 

slsDetectorSoftware/gotthardDetectorServer/gitInfo.txt

@@ -1,9 +1,9 @@
 Path: slsDetectorsPackage/slsDetectorSoftware/gotthardDetectorServer 
 URL: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
 Repository Root: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
-Repsitory UUID: 675d69392a6497d42b23057c7c8783c8dad768d0 
-Revision: 223 
-Branch: 3.1.0-rc 
+Repsitory UUID: d69d69e8928f90b053a0e5ffccb9cfc4e9c5f960 
+Revision: 225 
+Branch: 3.1.4-rc 
 Last Changed Author: Dhanya_Thattil 
-Last Changed Rev: 3447 
-Last Changed Date: 2018-02-27 14:04:08.000000002 +0100 ./server_funcs.c
+Last Changed Rev: 3483 
+Last Changed Date: 2018-07-25 14:56:37.000000002 +0200 ./firmware_funcs.c

slsDetectorSoftware/gotthardDetectorServer/gitInfoGotthard.h

@@ -1,6 +1,6 @@
 #define GITURL "git@github.com:slsdetectorgroup/slsDetectorPackage.git"
-#define GITREPUUID "675d69392a6497d42b23057c7c8783c8dad768d0"
+#define GITREPUUID "d69d69e8928f90b053a0e5ffccb9cfc4e9c5f960"
 #define GITAUTH "Dhanya_Thattil"
-#define GITREV 0x3447
-#define GITDATE 0x20180227
-#define GITBRANCH "3.1.0-rc"
+#define GITREV 0x3483
+#define GITDATE 0x20180725
+#define GITBRANCH "3.1.4-rc"

slsDetectorSoftware/gotthardDetectorServer/server_defs.h

@@ -54,7 +54,7 @@
 #define DEBUGOUT
 #endif
 
-#define CLK_FREQ 32.1E+6
+#define CLK_FREQ 32.007729
 
 
 #endif

slsDetectorSoftware/jungfrauDetectorServer/RegisterDefs.h

@@ -75,8 +75,8 @@
 #define TIME_FROM_START_MSB_REG   		(0x11 << 11)
 
 /* Get Delay 64 bit register */
-#define GET_DELAY_LSB_REG     			(0x12 << 11)
-#define GET_DELAY_MSB_REG     			(0x13 << 11)
+#define GET_DELAY_LSB_REG     			(0x12 << 11) 		// different kind of delay
+#define GET_DELAY_MSB_REG     			(0x13 << 11)		// different kind of delay
 
 /* Get Cycles 64 bit register */
 #define GET_CYCLES_LSB_REG    			(0x14 << 11)
@@ -321,8 +321,8 @@
 
 
 /* Set Delay 64 bit register */
-#define SET_DELAY_LSB_REG     			(0x60 << 11)
-#define SET_DELAY_MSB_REG     			(0x61 << 11)
+#define SET_DELAY_LSB_REG     			(0x60 << 11)  // different kind of delay
+#define SET_DELAY_MSB_REG     			(0x61 << 11)  // different kind of delay
 
 /* Set Cycles 64 bit register */
 #define SET_CYCLES_LSB_REG    			(0x62 << 11)

slsDetectorSoftware/jungfrauDetectorServer/gitInfo.txt

@@ -1,9 +1,9 @@
 Path: slsDetectorsPackage/slsDetectorSoftware/jungfrauDetectorServer 
 URL: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
 Repository Root: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
-Repsitory UUID: 8b02aa9e91bbee0470492dcf1ff67415851e14fa 
-Revision: 117 
-Branch: 3.1.0-rc 
-Last Changed Author: Erik_Frojdh 
-Last Changed Rev: 3455 
-Last Changed Date: 2018-03-08 16:44:32.000000002 +0100 ./RegisterDefs.h
+Repsitory UUID: e599bfe56f512ea6a262483f61ffd8d67d6c6fcd 
+Revision: 119 
+Branch: 3.1.3 
+Last Changed Author: Dhanya_Thattil 
+Last Changed Rev: 3475 
+Last Changed Date: 2018-06-28 15:11:57.000000002 +0200 ./RegisterDefs.h

slsDetectorSoftware/jungfrauDetectorServer/gitInfoJungfrau.h

@@ -1,6 +1,6 @@
 #define GITURL "git@github.com:slsdetectorgroup/slsDetectorPackage.git"
-#define GITREPUUID "8b02aa9e91bbee0470492dcf1ff67415851e14fa"
-#define GITAUTH "Erik_Frojdh"
-#define GITREV 0x3455
-#define GITDATE 0x20180308
-#define GITBRANCH "3.1.0-rc"
+#define GITREPUUID "e599bfe56f512ea6a262483f61ffd8d67d6c6fcd"
+#define GITAUTH "Dhanya_Thattil"
+#define GITREV 0x3475
+#define GITDATE 0x20180628
+#define GITBRANCH "3.1.3"

slsDetectorSoftware/jungfrauDetectorServer/slsDetectorFunctionList.c

@@ -155,18 +155,21 @@ int testBus() {
 	printf("\nTesting Bus...\n");
 
 	int ret = OK;
-	u_int32_t addr = SET_DELAY_LSB_REG;
+	u_int32_t addr = SET_TRIGGER_DELAY_LSB_REG;
 	int times = 1000 * 1000;
 	int i = 0;
 
 	for (i = 0; i < times; ++i) {
 		bus_w(addr, i * 100);
-		if (i * 100 != bus_r(SET_DELAY_LSB_REG)) {
-			cprintf(RED,"ERROR: Mismatch! Wrote 0x%x, read 0x%x\n", i * 100, bus_r(SET_DELAY_LSB_REG));
+		if (i * 100 != bus_r(addr)) {
+			cprintf(RED,"ERROR: Mismatch! Wrote 0x%x, read 0x%x\n",
+					i * 100, bus_r(addr));
 			ret = FAIL;
 		}
 	}
 
+	bus_w(addr, 0);
+
 	if (ret == OK)
 		printf("Successfully tested bus %d times\n", times);
 	return ret;
@@ -487,9 +490,11 @@ int adcPhase(int st){ /**carlos needed clkphase 1 and 2?  cehck with Aldo */
 	printf("Setting ADC Phase to %d\n",st);
 	if (st > 65535 || st < -65535)
 		return clkPhase[0];
-	clkPhase[1] = st - clkPhase[0];
 
-	printf(" phase %d\n", clkPhase[1] );
+	clkPhase[1] = st - clkPhase[0];
+	if (clkPhase[1] == 0)
+	    return clkPhase[0];
+
 	configurePll();
 	clkPhase[0] = st;
 	return clkPhase[0];
@@ -695,12 +700,12 @@ int64_t getTimeLeft(enum timerIndex ind){
 		retval = get64BitReg(GET_PERIOD_LSB_REG, GET_PERIOD_MSB_REG) / (1E-3 * CLK_SYNC);
 		printf("Getting period left: %lldns\n", (long long int)retval);
 		break;
-
+/*
 	case DELAY_AFTER_TRIGGER:
-		retval = get64BitReg(GET_DELAY_LSB_REG, GET_DELAY_MSB_REG) / (1E-3 * CLK_SYNC);
+		retval = get64BitReg(xxx) / (1E-3 * CLK_SYNC);
 		printf("Getting delay left: %lldns\n", (long long int)retval);
 		break;
-
+*/
 	case CYCLES_NUMBER:
 		retval = get64BitReg(GET_CYCLES_LSB_REG, GET_CYCLES_MSB_REG);
 		printf("Getting number of cycles left: %lld\n", (long long int)retval);
@@ -1230,8 +1235,12 @@ void configurePll() {
 #endif
 	u_int32_t val;
 	int32_t phase=0, inv=0;
+	// ensuring PLL is never configured with same phase
+    if (clkPhase[1] == 0) {
+        return;
+    }
 
-	printf(" phase in %d\n", clkPhase[1]);
+	printf("Configuring PLL with phase in %d\n", clkPhase[1]);
 	if (clkPhase[1]>0) {
 		inv=0;
 		phase=clkPhase[1];

slsDetectorSoftware/jungfrauDetectorServer/slsDetectorServer_defs.h

@@ -101,8 +101,8 @@ enum NETWORKINDEX           { TXN_FRAME };
 #define CONFIG_QUARTER_SPEED		(CONFIG_TDMA_DISABLE_VAL + CONFIG_QUARTER_SPEED_10MHZ_VAL + CONFIG_MODE_1_X_10GBE_VAL)
 #define ADC_OFST_HALF_SPEED_VAL		(0x20) //adc pipeline
 #define ADC_OFST_QUARTER_SPEED_VAL	(0x0f)
-#define ADC_PHASE_HALF_SPEED 		(0x41)
-#define ADC_PHASE_QUARTER_SPEED 	(0x19)
+#define ADC_PHASE_HALF_SPEED 		(0x48) //72
+#define ADC_PHASE_QUARTER_SPEED 	(0x48) //72
 
 /* Maybe not required for jungfrau */
 #define NTRIMBITS 					(6)

slsDetectorSoftware/multiSlsDetector/multiSlsDetector.cpp

@@ -1974,10 +1974,26 @@ void multiSlsDetector::resetFinalDataQueue() {
    GATE_INTEGRATED_TIME
    }
  */
-int64_t multiSlsDetector::setTimer(timerIndex index, int64_t t){
+int64_t multiSlsDetector::setTimer(timerIndex index, int64_t t, int imod){
 
 	int64_t ret=-100;
 
+	// single (for gotthard 25 um)
+	if (imod != -1) {
+		if (imod >= 0 && imod < thisMultiDetector->numberOfDetectors) {
+			if (detectors[imod]) {
+				ret = detectors[imod]->setTimer(index,t,imod);
+				if(detectors[imod]->getErrorMask())
+					setErrorMask(getErrorMask()|(1<<imod));
+				return ret;
+			}
+			return -1;
+		}
+		return -1;
+	}
+
+
+	// multi
 	if(!threadpool){
 		cout << "Error in creating threadpool. Exiting" << endl;
 		return -1;
@@ -1987,8 +2003,8 @@ int64_t multiSlsDetector::setTimer(timerIndex index, int64_t t){
 		for(int idet=0; idet<thisMultiDetector->numberOfDetectors; ++idet){
 			if(detectors[idet]){
 				iret[idet]= new int64_t(-1);
-				Task* task = new Task(new func2_t<int64_t,timerIndex,int64_t>(&slsDetector::setTimer,
-						detectors[idet],index,t,iret[idet]));
+				Task* task = new Task(new func3_t<int64_t,timerIndex,int64_t,int>(&slsDetector::setTimer,
+						detectors[idet],index,t,imod,iret[idet]));
 				threadpool->add_task(task);
 			}
 		}

slsDetectorSoftware/multiSlsDetector/multiSlsDetector.h

@@ -688,9 +688,10 @@ class multiSlsDetector  : public slsDetectorUtils {
       set/get timer value
       \param index timer index
       \param t time in ns or number of...(e.g. frames, gates, probes)
+      \param imod module number (gotthard delay can have different values)
       \returns timer set value in ns or number of...(e.g. frames, gates, probes)
   */
-  int64_t setTimer(timerIndex index, int64_t t=-1);
+  int64_t setTimer(timerIndex index, int64_t t=-1, int imod = -1);
   /** 
       set/get timer value
       \param index timer index

slsDetectorSoftware/slsDetector/gitInfoLib.h

@@ -1,6 +1,6 @@
 #define GITURL "git@github.com:slsdetectorgroup/slsDetectorPackage.git"
-#define GITREPUUID "b389402d647e939342dbb2c9317c688c0eb6b105"
-#define GITAUTH "Erik_Frojdh"
-#define GITREV 0x3458
-#define GITDATE 0x20180312
-#define GITBRANCH "3.1.0-rc"
+#define GITREPUUID "1b92b01a466aa1986b8198700274af75477a1e54"
+#define GITAUTH "Dhanya_Thattil"
+#define GITREV 0x3492
+#define GITDATE 0x20180817
+#define GITBRANCH "3.1.4"

slsDetectorSoftware/slsDetector/slsDetector.cpp

@@ -270,7 +270,10 @@ slsDetector::~slsDetector(){
   else
     printf("Shared memory %d detached\n", shmId);
 #endif
-delete thisReceiver;
+  if(controlSocket) delete controlSocket;
+  if(stopSocket) delete stopSocket;
+  if(dataSocket) delete dataSocket;
+if(thisReceiver)    delete thisReceiver;
 };
 
 slsDetector::slsDetector(int pos, char *name, int id, int cport,multiSlsDetector *p) : slsDetectorUtils(),
@@ -1318,6 +1321,26 @@ string slsDetector::checkOnline() {
       disconnectControl();
 #ifdef VERBOSE
       std::cout<< "online!" << std::endl;
+#endif
+    }
+  }
+  //still cannot connect to socket, controlSocket=0
+  if(stopSocket){
+    if (connectStop() == FAIL) {
+      stopSocket->SetTimeOut(5);
+      thisDetector->onlineFlag=OFFLINE_FLAG;
+      delete stopSocket;
+      stopSocket=NULL;
+      retval = string(thisDetector->hostname);
+#ifdef VERBOSE
+      std::cout<< "stop offline!" << std::endl;
+#endif
+    }  else {
+      thisDetector->onlineFlag=ONLINE_FLAG;
+      stopSocket->SetTimeOut(100);
+      disconnectStop();
+#ifdef VERBOSE
+      std::cout<< "stop online!" << std::endl;
 #endif
     }
   }
@@ -3698,6 +3721,9 @@ slsDetectorDefs::detectorSettings slsDetector::setSettings( detectorSettings ise
 	std::cout<< "slsDetector setSettings "<< std::endl;
 #endif
 
+	if (isettings == -1)
+		return getSettings(imod);
+
 	//only set client shared memory variable for Eiger, settings threshold loads the module data (trimbits, dacs etc.)
 	if (thisDetector->myDetectorType == EIGER) {
 		switch(isettings) {
@@ -4583,7 +4609,7 @@ int slsDetector::startAndReadAllNoWait(){
    GATE_INTEGRATED_TIME
    }
 */
-int64_t slsDetector::setTimer(timerIndex index, int64_t t){
+int64_t slsDetector::setTimer(timerIndex index, int64_t t, int imod){
 
 
 	int fnum=F_SET_TIMER,fnum2=F_SET_RECEIVER_TIMER;
@@ -7392,7 +7418,7 @@ int slsDetector::programFPGA(string fname){
 #endif
 	if (thisDetector->onlineFlag==ONLINE_FLAG) {
 		if (connectControl() == OK){
-			controlSocket->SendDataOnly(&fnum,sizeof(fnum));cprintf(BG_RED,"size of filesize:%lu\n",sizeof(filesize));
+			controlSocket->SendDataOnly(&fnum,sizeof(fnum));
 			controlSocket->SendDataOnly(&filesize,sizeof(filesize));
 			//check opening error
 			controlSocket->ReceiveDataOnly(&ret,sizeof(ret));

slsDetectorSoftware/slsDetector/slsDetector.h

@@ -1205,9 +1205,10 @@ class slsDetector : public slsDetectorUtils, public energyConversion {
       set/get timer value
       \param index timer index
       \param t time in ns or number of...(e.g. frames, gates, probes)
+      \param imod module number (pointless in slsDetector)
       \returns timer set value in ns or number of...(e.g. frames, gates, probes)
   */
-  int64_t setTimer(timerIndex index, int64_t t=-1);
+  int64_t setTimer(timerIndex index, int64_t t=-1, int imod = -1);
 
   /** 
       get current timer value

slsDetectorSoftware/slsDetector/slsDetectorBase.h

@@ -369,16 +369,17 @@ class slsDetectorBase :  public virtual slsDetectorDefs, public virtual errorDef
      set/get timer value
      \param index timer index
      \param t time in ns or number of...(e.g. frames, gates, probes)
+     \param imod module number
      \returns timer set value in ns or number of...(e.g. frames, gates, probes)
   */
-  virtual int64_t setTimer(timerIndex index, int64_t t=-1)=0;
-  int64_t setExposureTime(int64_t t=-1){return setTimer(ACQUISITION_TIME,t);};
-  int64_t setSubFrameExposureTime(int64_t t=-1){return setTimer(SUBFRAME_ACQUISITION_TIME,t);};
-  int64_t setExposurePeriod(int64_t t=-1){return setTimer(FRAME_PERIOD,t);};
-  int64_t setDelayAfterTrigger(int64_t t=-1){return setTimer(DELAY_AFTER_TRIGGER,t);};
-  int64_t setNumberOfGates(int64_t t=-1){return setTimer(GATES_NUMBER,t);};
-  int64_t setNumberOfFrames(int64_t t=-1){return setTimer(FRAME_NUMBER,t);};
-  int64_t setNumberOfCycles(int64_t t=-1){return setTimer(CYCLES_NUMBER,t);};
+  virtual int64_t setTimer(timerIndex index, int64_t t=-1, int imod = -1) = 0;
+  int64_t setExposureTime(int64_t t=-1, int imod = -1){return setTimer(ACQUISITION_TIME,t,imod);};
+  int64_t setSubFrameExposureTime(int64_t t=-1, int imod = -1){return setTimer(SUBFRAME_ACQUISITION_TIME,t,imod);};
+  int64_t setExposurePeriod(int64_t t=-1, int imod = -1){return setTimer(FRAME_PERIOD,t,imod);};
+  int64_t setDelayAfterTrigger(int64_t t=-1, int imod = -1){return setTimer(DELAY_AFTER_TRIGGER,t,imod);};
+  int64_t setNumberOfGates(int64_t t=-1, int imod = -1){return setTimer(GATES_NUMBER,t,imod);};
+  int64_t setNumberOfFrames(int64_t t=-1, int imod = -1){return setTimer(FRAME_NUMBER,t,imod);};
+  int64_t setNumberOfCycles(int64_t t=-1, int imod = -1){return setTimer(CYCLES_NUMBER,t,imod);};
 
 
   /** sets/gets the value of important readout speed parameters

slsDetectorSoftware/slsDetector/slsDetectorCommand.cpp

@@ -710,7 +710,7 @@ slsDetectorCommand::slsDetectorCommand(slsDetectorUtils *det)  {
 	 */
 
 	/*! \page config
-   - <b>clkdivider [i]</b> sets/gets the readout clock divider. EIGER, JUNGFRAU [0(fast speed), 1(half speed), 2(quarter speed)]. MYTHEN[???]. \c Returns \c (int)
+   - <b>clkdivider [i]</b> sets/gets the readout clock divider. EIGER, JUNGFRAU [0(fast speed), 1(half speed), 2(quarter speed)]. Jungfrau, full speed is not implemented and overwrites adcphase to recommended default. MYTHEN[???]. \c Returns \c (int)
 	 */
 	descrToFuncMap[i].m_pFuncName="clkdivider"; //
 	descrToFuncMap[i].m_pFuncPtr=&slsDetectorCommand::cmdSpeed;
@@ -766,7 +766,7 @@ slsDetectorCommand::slsDetectorCommand(slsDetectorUtils *det)  {
 	++i;
 
 	/*! \page config
-   - <b>adcphase [i]</b> Sets/gets the ADC clock frequency in MHz. For the new chiptestboard!\c Returns \c (int)
+   - <b>adcphase [i]</b> Sets/gets phase of the sampling clock. For JUNGFRAU, setting speed (clkdivider) overwrites adcphase to its default recommended value. (Not for EIGER) \c Returns \c (int)
 	 */
 	descrToFuncMap[i].m_pFuncName="adcphase"; //
 	descrToFuncMap[i].m_pFuncPtr=&slsDetectorCommand::cmdSpeed;
@@ -5464,11 +5464,8 @@ string slsDetectorCommand::cmdTimer(int narg, char *args[], int action) {
 		else
 			return string("cannot scan timer value ")+string(args[1]);
 		if (index==ACQUISITION_TIME || index==SUBFRAME_ACQUISITION_TIME || index==FRAME_PERIOD || index==DELAY_AFTER_TRIGGER) {
-			// 	t=(int64_t)(val*1E+9); for precision of eg.0.0000325, following done
-			val*=1E9;
-			t = (int64_t)val;
-			if(fabs(val-t))		// to validate precision loss
-				t = t + val - t; //even t += vak-t loses precision
+			// 	+0.5 for precision of eg.0.0000325
+			t = ( val * 1E9 + 0.5);
 		}else t=(int64_t)val;
 	}
 
@@ -5685,9 +5682,6 @@ string slsDetectorCommand::cmdSpeed(int narg, char *args[], int action) {
 			return string("cannot scan speed value ")+string(args[1]);
 
 	}
-	// -1 could work
-	else if (cmd=="adcphase")
-	    t = 65536;
 
 	myDet->setOnline(ONLINE_FLAG);
 
@@ -5707,21 +5701,23 @@ string slsDetectorCommand::helpSpeed(int narg, char *args[], int action) {
 	ostringstream os;
 	if (action==PUT_ACTION || action==HELP_ACTION) {
 
-		os << "clkdivider c  \t sets readout clock divider" << std::endl;
+		os << "clkdivider c  \t sets readout clock divider. For Jungfrau, it also overwrites adcphase to recommended default" << std::endl;
 		os << "setlength  c\t sets the length of the set/reset signals (in clock cycles)" << std::endl;
 		os << "waitstates c \t sets the waitstates of the bus interface" << std::endl;
 		os << "totdivider  c\t sets the clock divider in tot mode" << std::endl;
 		os << "totdutycycle  c\t sets the duty cycle of the tot clock" << std::endl;
+		os << "adcphase  c\t Sets phase of the sampling clock. For JUNGFRAU, setting speed (clkdivider) overwrites adcphase to its default recommended value. (Not for EIGER)" << std::endl;
 		os << std::endl;
 
 	}
 	if (action==GET_ACTION || action==HELP_ACTION) {
 
-		os << "clkdivider  \t gets readout clock divider" << std::endl;
+		os << "clkdivider  \t gets readout clock divider. For Jungfrau, it also overwrites adcphase to recommended default" << std::endl;
 		os << "setlength  \t gets the length of the set/reset signals (in clock cycles)" << std::endl;
 		os << "waitstates  \t gets the waitstates of the bus interface" << std::endl;
 		os << "totdivider \t gets the clock divider in tot mode" << std::endl;
 		os << "totdutycycle \t gets the duty cycle of the tot clock" << std::endl;
+        os << "totdutycycle \t gets phase of the sampling clock. For JUNGFRAU, setting speed (clkdivider) overwrites adcphase to its default recommended value. (Not for EIGER)" << std::endl;
 		os << std::endl;
 
 	}

slsDetectorSoftware/slsDetector/slsDetectorUsers.cpp

@@ -151,43 +151,58 @@ int slsDetectorUsers::setThresholdEnergy(int e_eV){
   return myDetector->setThresholdEnergy(e_eV);
 }
 
-double slsDetectorUsers::setExposureTime(double t, bool inseconds){
-  int64_t tms = (int64_t)(t * (1E+9));
-  if (t < 0) tms = -1;
+double slsDetectorUsers::setExposureTime(double t, bool inseconds, int imod){
   if(!inseconds)
-    return myDetector->setExposureTime((int64_t)t);
-  else
-    return  ((1E-9) * (double)myDetector->setExposureTime(tms));
-}
-
-double slsDetectorUsers::setExposurePeriod(double t, bool inseconds){
-  int64_t tms = (int64_t)(t * (1E+9));
+    return myDetector->setExposureTime((int64_t)t,imod);
+  else {
+	  // + 0.5 to round for precision lost from converting double to int64_t
+	  int64_t tms = (int64_t)(t * (1E+9) + 0.5);
 	  if (t < 0) tms = -1;
-  if(!inseconds)
-    return myDetector->setExposurePeriod((int64_t)t);
-  else
-    return  ((1E-9) * (double)myDetector->setExposurePeriod(tms));
+	  tms = myDetector->setExposureTime(tms,imod);
+	  if (tms < 0)
+		  return -1;
+	  return  ((1E-9) * (double)tms);
+  }
 }
 
-double slsDetectorUsers::setDelayAfterTrigger(double t, bool inseconds){
-  int64_t tms = (int64_t)(t * (1E+9));
+double slsDetectorUsers::setExposurePeriod(double t, bool inseconds, int imod){
+  if(!inseconds)
+    return myDetector->setExposurePeriod((int64_t)t,imod);
+  else {
+	  // + 0.5 to round for precision lost from converting double to int64_t
+	  int64_t tms = (int64_t)(t * (1E+9) + 0.5);
 	  if (t < 0) tms = -1;
+	  tms = myDetector->setExposurePeriod(tms,imod);
+	  if (tms < 0)
+		  return -1;
+	  return  ((1E-9) * (double)tms);
+  }
+}
+
+double slsDetectorUsers::setDelayAfterTrigger(double t, bool inseconds, int imod){
   if(!inseconds)
-    return myDetector->setDelayAfterTrigger((int64_t)t);
-  else
-    return  ((1E-9) * (double)myDetector->setDelayAfterTrigger(tms));
+    return myDetector->setDelayAfterTrigger((int64_t)t,imod);
+  else {
+	  // + 0.5 to round for precision lost from converting double to int64_t
+	  int64_t tms = (int64_t)(t * (1E+9) + 0.5);
+	  if (t < 0) tms = -1;
+	  tms = myDetector->setDelayAfterTrigger(tms,imod);
+	  if (tms < 0)
+		  return -1;
+	  return  ((1E-9) * (double)tms);
+  }
 }
 
-int64_t slsDetectorUsers::setNumberOfGates(int64_t t){
-  return myDetector->setNumberOfGates(t);
+int64_t slsDetectorUsers::setNumberOfGates(int64_t t, int imod){
+  return myDetector->setNumberOfGates(t,imod);
 } 
 
-int64_t slsDetectorUsers::setNumberOfFrames(int64_t t){
-  return myDetector->setNumberOfFrames(t);
+int64_t slsDetectorUsers::setNumberOfFrames(int64_t t, int imod){
+  return myDetector->setNumberOfFrames(t,imod);
 }
 
-int64_t slsDetectorUsers::setNumberOfCycles(int64_t t){
-  return myDetector->setNumberOfCycles(t);
+int64_t slsDetectorUsers::setNumberOfCycles(int64_t t, int imod){
+  return myDetector->setNumberOfCycles(t,imod);
 }
   
 int slsDetectorUsers::setTimingMode(int pol){

slsDetectorSoftware/slsDetector/slsDetectorUsers.h

@@ -270,7 +270,7 @@ class slsDetectorUsers
   */
    int getDetectorSize(int &x0, int &y0, int &nx, int &ny);
   /**
-     @short setsthe maximum detector size
+     @short gets the maximum detector size
      \param x0 horizontal position origin in channel number 
      \param y0 vertical position origin in channel number 
      \param nx number of channels in horiziontal
@@ -315,47 +315,53 @@ class slsDetectorUsers
         @short set/get exposure time value
         \param t time in sn  (-1 gets)
         \param inseconds true if the value is in s, else ns
+        \param imod module number (-1 for all)
         \returns timer set value in ns, or s if specified
     */
 
-   double setExposureTime(double t=-1, bool inseconds=false);
+   double setExposureTime(double t=-1, bool inseconds=false, int imod = -1);
 
     /**
          @short set/get exposure period
         \param t time in ns   (-1 gets)
         \param inseconds true if the value is in s, else ns
+        \param imod module number (-1 for all)
         \returns timer set value in ns, or s if specified
     */
-   double setExposurePeriod(double t=-1, bool inseconds=false);
+   double setExposurePeriod(double t=-1, bool inseconds=false, int imod = -1);
 
     /**
          @short set/get delay after trigger
         \param t time in ns   (-1 gets)
         \param inseconds true if the value is in s, else ns
+        \param imod module number (-1 for all)
         \returns timer set value in ns, or s if specified
     */
-   double setDelayAfterTrigger(double t=-1, bool inseconds=false);
+   double setDelayAfterTrigger(double t=-1, bool inseconds=false, int imod = -1);
 
   /** 
        @short set/get number of gates
       \param t number of gates  (-1 gets)
+      \param imod module number (-1 for all)
       \returns number of gates
   */
-   int64_t setNumberOfGates(int64_t t=-1); 
+   int64_t setNumberOfGates(int64_t t=-1, int imod = -1);
   
   /** 
        @short set/get number of frames i.e. number of exposure per trigger
       \param t number of frames  (-1 gets) 
+      \param imod module number (-1 for all)
       \returns number of frames
   */
-   int64_t setNumberOfFrames(int64_t t=-1);
+   int64_t setNumberOfFrames(int64_t t=-1, int imod = -1);
 
   /** 
        @short set/get number of cycles i.e. number of triggers
       \param t number of frames  (-1 gets) 
+      \param imod module number (-1 for all)
       \returns number of frames
   */
-   int64_t setNumberOfCycles(int64_t t=-1);
+   int64_t setNumberOfCycles(int64_t t=-1, int imod = -1);
   
 
  /** 

slsDetectorSoftware/slsDetectorServer/slsDetectorServer_funcs.c

@@ -39,6 +39,9 @@ char mess[MAX_STR_LENGTH];
 int dataBytes = 10;
 int isControlServer = 0;
 int debugflag = 0;
+#ifdef EIGERD
+uint32_t dhcpipad = 0;
+#endif
 
 /* initialization functions */
 
@@ -64,6 +67,9 @@ void init_detector(int controlserver) {
 	if (controlserver) {
 	    isControlServer = 1;
 		initControlServer();
+#ifdef EIGERD
+		dhcpipad = getDetectorIP();
+#endif
 	}
 	else initStopServer();
 #endif
@@ -2621,6 +2627,15 @@ int get_time_left(int file_des) {
 	printf("getting time left on timer %d \n",ind);
 #endif
 #ifdef SLS_DETECTOR_FUNCTION_LIST
+
+#ifdef JUNGFRAUD
+	if (ind == DELAY_AFTER_TRIGGER) {
+		ret = FAIL;
+		sprintf(mess,"Timer Left Index (%d) is not implemented for this release.\n", (int)ind);
+		cprintf(RED, "%s", mess);
+	} else {
+#endif
+
 		switch(ind) {
 #ifdef MYTHEND
 		case PROBES_NUMBER:
@@ -2651,6 +2666,11 @@ int get_time_left(int file_des) {
 #ifdef VERBOSE
 		printf("Time left on timer %d is %lld\n",ind, retval);
 #endif
+
+#ifdef JUNGFRAUD
+	}	// end of if (ind == DELAY_AFTER_TRIGGER)
+#endif
+
 #endif
 	if (ret==OK && differentClients)
 		ret=FORCE_UPDATE;
@@ -2988,7 +3008,7 @@ int set_speed(int file_des) {
 #ifdef JUNGFRAUD
 		case ADC_PHASE:
 			retval = adcPhase(val);
-            if ((val != 65536) && (retval!=val) && (val>=0)) {
+            if ((val != 100000) && (retval!=val) && (val>=0)) {
                 ret=FAIL;
                 sprintf(mess,"could not change set adc phase: should be %d but is %d \n", val, retval);
                 cprintf(RED, "Warning: %s", mess);
@@ -3488,16 +3508,19 @@ int configure_mac(int file_des) {
 			        printf("WARNING: Matched detectormac to the hardware mac now\n");
 			        printf("*************************************************\n");
 			    }
+
+			    // always remember the ip sent from the client (could be for 10g(if not dhcp))
+			    if (detipad != getDetectorIP())
+			        dhcpipad = detipad;
+
 			    //only for 1Gbe
 			    if(!enableTenGigabitEthernet(-1)){
-			        if (detipad != getDetectorIP()){
 			        printf("*************************************************\n");
-			            printf("WARNING: actual detector ip address %x does not match the one from client %x\n",getDetectorIP(),detipad);
+                    printf("WARNING: Using DHCP IP for Configuring MAC\n");
+                    printf("*************************************************\n");
                     detipad = getDetectorIP();
-			            printf("WARNING: Matched detector ip to the hardware ip now\n");
-			            printf("*************************************************\n");
-			        }
-			    }
+			    } else
+			        detipad = dhcpipad;
 #endif
 				retval=configureMAC(ipad,imacadd,idetectormacadd,detipad,udpport,udpport2,0);	//digitalTestBit);
 				if(retval==-1) {

slsDetectorSoftware/slsReceiverInterface/receiverInterface.cpp

@@ -15,9 +15,7 @@ receiverInterface::receiverInterface(MySocketTCP *socket):dataSocket(socket){}
 
 
 
-receiverInterface::~receiverInterface(){
-	delete dataSocket;
-}
+receiverInterface::~receiverInterface(){}
 
 
 

slsDetectorSoftware/threadFiles/Task.h

@@ -110,7 +110,7 @@ class SuperTask:  public virtual slsDetectorDefs {
 public:
 	SuperTask():
 		m1(0),m2(0),m3(0),m4(0),m5(0),m6(0),m7(0),m8(0),m9(0),m10(0),m11(0),m12(0),m13(0),m14(0),m15(0),m16(0),m17(0),m18(0){};
-	~SuperTask(){};
+	virtual ~SuperTask(){};
 protected:
 	/** Function signature defined
 	 * First argument is Return type, the remaining are arguments
@@ -127,7 +127,7 @@ protected:
 	func2_t <int,				string,int>* 					m10;
 	func2_t <dacs_t,			dacIndex,int>* 					m11;
 	func2_t <detectorSettings,	detectorSettings,int>* 			m12;
-	func2_t <int64_t,			timerIndex,int64_t>* 			m13;
+	func3_t <int64_t,			timerIndex,int64_t,int>* 		m13;
 	func2_t <string,			networkParameter,string>* 		m14;
 	func3_t <int,				int,int,int>* 					m15;
 	func4_t <int,				trimMode,int,int,int>* 			m16;
@@ -152,14 +152,39 @@ public:
 	Task(func2_t <int,				string,int>* t):						SuperTask(),fnum(10){m10 = t;};
 	Task(func2_t <dacs_t,			dacIndex,int>* t):                  	SuperTask(),fnum(11){m11 = t;};
 	Task(func2_t <detectorSettings,	detectorSettings,int>* t):				SuperTask(),fnum(12){m12 = t;};
-	Task(func2_t <int64_t,			timerIndex,int64_t>* t):				SuperTask(),fnum(13){m13 = t;};
+	Task(func3_t <int64_t,			timerIndex,int64_t,int>* t):			SuperTask(),fnum(13){m13 = t;};
 	Task(func2_t <string,			networkParameter,string>* t):			SuperTask(),fnum(14){m14 = t;};
 	Task(func3_t <int,				int,int,int>* t): 						SuperTask(),fnum(15){m15 = t;};
 	Task(func4_t <int,				trimMode,int,int,int>* t):				SuperTask(),fnum(16){m16 = t;};
 	Task(func4_t <int,				int,int,detectorSettings,int>* t): 		SuperTask(),fnum(17){m17 = t;};
 	Task(func4_t <dacs_t,			dacs_t,dacIndex,int,int>* t):       	SuperTask(),fnum(18){m18 = t;};
 
-	~Task(){}
+	virtual ~Task(){
+        switch(fnum) {
+        case 1: delete m1;  break;
+        case 2: delete m2;  break;
+        case 3: delete m3;  break;
+        case 4: delete m4;  break;
+        case 5: delete m5;  break;
+        case 6: delete m6;  break;
+        case 7: delete m7;  break;
+        case 8: delete m8;  break;
+        case 9: delete m9;  break;
+        case 10: delete m10;  break;
+        case 11: delete m11;  break;
+        case 12: delete m12;  break;
+        case 13: delete m13;  break;
+        case 14: delete m14;  break;
+        case 15: delete m15;  break;
+        case 16: delete m16;  break;
+        case 17: delete m17;  break;
+        case 18: delete m18;  break;
+        default:
+            cprintf(RED, "Error: Task not defined. Abort!\n");
+            break;
+        }
+
+	};
 
 	void operator()(){
 		switch(fnum) {

slsReceiverSoftware/gitInfo.txt

@@ -1,9 +1,9 @@
 Path: slsDetectorsPackage/slsReceiverSoftware 
 URL: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
 Repository Root: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
-Repsitory UUID: b389402d647e939342dbb2c9317c688c0eb6b105 
-Revision: 708 
-Branch: 3.1.0-rc 
-Last Changed Author: Erik_Frojdh 
-Last Changed Rev: 3458 
-Last Changed Date: 2018-03-09 12:23:14.000000002 +0100 ./src/Listener.cpp
+Repsitory UUID: 1b92b01a466aa1986b8198700274af75477a1e54 
+Revision: 715 
+Branch: 3.1.4 
+Last Changed Author: Dhanya_Thattil 
+Last Changed Rev: 3492 
+Last Changed Date: 2018-08-17 16:36:25.000000002 +0200 ./src/utilities.cpp

slsReceiverSoftware/include/DataProcessor.h

@@ -198,9 +198,10 @@ class DataProcessor : private virtual slsReceiverDefs, public ThreadObject {
 
 	/**
 	 * End of Acquisition
+	 * @param anyPacketsCaught true if any packets are caught, else false
 	 * @param numf number of images caught
 	 */
-	void EndofAcquisition(uint64_t numf);
+	void EndofAcquisition(bool anyPacketsCaught, uint64_t numf);
 
 
  private:

slsReceiverSoftware/include/File.h

@@ -159,9 +159,10 @@ class File : private virtual slsReceiverDefs {
 
 	/**
 	 * End of Acquisition
+	 * @param anyPacketsCaught true if any packets are caught, else false
 	 * @param numf number of images caught
 	 */
-	virtual void EndofAcquisition(uint64_t numf) {
+	virtual void EndofAcquisition(bool anyPacketsCaught, uint64_t numf) {
 		cprintf(RED,"This is a generic function EndofAcquisition that should be overloaded by a derived class\n");
 	}
 

slsReceiverSoftware/include/HDF5File.h

@@ -111,9 +111,10 @@ class HDF5File : private virtual slsReceiverDefs, public File, public HDF5FileSt
 
 	/**
 	 * End of Acquisition
+	 * @param anyPacketsCaught true if any packets are caught, else false
 	 * @param numf number of images caught
 	 */
-	void EndofAcquisition(uint64_t numf);
+	void EndofAcquisition(bool anyPacketsCaught, uint64_t numf);
 
 	/**
 	 * Create Virtual File
@@ -180,5 +181,8 @@ class HDF5File : private virtual slsReceiverDefs, public File, public HDF5FileSt
 	/** Dataset array for parameters */
 	DataSet* dataset_para[HDF5FileStatic::NumberofParameters];
 
+	/** Number of Images (including extended during acquisition) */
+	uint64_t extNumImages;
+
 };
 #endif

slsReceiverSoftware/include/HDF5FileStatic.h

@@ -112,7 +112,7 @@ public:
 			}
 		} catch(Exception error) {
 			cprintf(RED,"Error in closing HDF5 handles of index %d\n", ind);
-			error.printError();
+			error.printErrorStack();
 		}
 	}
 
@@ -130,7 +130,7 @@ public:
 			}
 		} catch(Exception error) {
 			cprintf(RED,"Error in closing master HDF5 handles\n");
-			error.printError();
+			error.printErrorStack();
 		}
 	}
 
@@ -177,7 +177,7 @@ public:
 		}
 		catch(Exception error){
 			cprintf(RED,"Error in writing to file in object %d\n",ind);
-			error.printError();
+			error.printErrorStack();
 			return 1;
 		}
 		return 0;
@@ -187,6 +187,12 @@ public:
 
 	/**
 	 * Write Parameter Arrays as datasets (to virtual file)
+	 * @param ind self index
+	 * @param dpace_para parameter dataspace
+	 * @param fnum frame number current
+	 * @param dset_para parameter dataset
+	 * @param header image header
+	 * @returns 0 for success and 1 for fail
 	 */
 	static int WriteParameterDatasets(int ind, DataSpace* dspace_para, uint64_t fnum,
 			DataSet* dset_para[],sls_detector_header* header)
@@ -213,12 +219,50 @@ public:
 		}
 		catch(Exception error){
 			cprintf(RED,"Error in writing parameters to file in object %d\n",ind);
-			error.printError();
+			error.printErrorStack();
 			return 1;
 		}
 		return 0;
 	}
 
+	/**
+	 * Extend datasets in #images dimension (x dimension)
+	 * @param ind self index
+	 * @param dpace data space pointer address
+	 * @param dset data set pointer
+	 * @param dspace_para parameter dataspace address pointer
+	 * @param dset dataset parameter pointer
+	 * @param initialNumImages initial number of images
+	 * @returns 0 for success and 1 for fail
+	 */
+	static int ExtendDataset(int ind, DataSpace*& dspace, DataSet* dset,
+			DataSpace*& dspace_para, DataSet* dset_para[],
+			uint64_t initialNumImages) {
+		try{
+			Exception::dontPrint(); //to handle errors
+
+			hsize_t dims[3];
+			dspace->getSimpleExtentDims(dims);
+			dims[0] += initialNumImages;
+
+			dset->extend(dims);
+			delete dspace;
+			dspace = new DataSpace(dset->getSpace());
+
+			hsize_t dims_para[1] = {dims[0]};
+			for (int i = 0; i < NumberofParameters; ++i)
+				dset_para[i]->extend(dims_para);
+			delete dspace_para;
+			dspace_para = new DataSpace(dset_para[0]->getSpace());
+
+		}
+		catch(Exception error){
+			cprintf(RED,"Error in extending dataset in object %d\n",ind);
+			error.printErrorStack();
+			return 1;
+		}
+		return 0;
+	}
 
 	/**
 	 * Create master file
@@ -246,9 +290,9 @@ public:
 			FileAccPropList flist;
 			flist.setFcloseDegree(H5F_CLOSE_STRONG);
 			if(!owenable)
-				fd = new H5File( fname.c_str(), H5F_ACC_EXCL, NULL, flist );
+				fd = new H5File( fname.c_str(), H5F_ACC_EXCL, FileCreatPropList::DEFAULT, flist );
 			else
-				fd = new H5File( fname.c_str(), H5F_ACC_TRUNC, NULL, flist );
+				fd = new H5File( fname.c_str(), H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, flist );
 
 			//variables
 			DataSpace dataspace = DataSpace (H5S_SCALAR);
@@ -328,7 +372,7 @@ public:
 
 		} catch(Exception error) {
 			cprintf(RED,"Error in creating master HDF5 handles\n");
-			error.printError();
+			error.printErrorStack();
 			return 1;
 		}
 		return 0;
@@ -374,9 +418,9 @@ public:
 			FileAccPropList fapl;
 			fapl.setFcloseDegree(H5F_CLOSE_STRONG);
 			if(!owenable)
-				fd = new H5File( fname.c_str(), H5F_ACC_EXCL, NULL,fapl );
+				fd = new H5File( fname.c_str(), H5F_ACC_EXCL, FileCreatPropList::DEFAULT,fapl );
 			else
-				fd = new H5File( fname.c_str(), H5F_ACC_TRUNC, NULL, fapl );
+				fd = new H5File( fname.c_str(), H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, fapl );
 
 			//attributes - version
 			double dValue=version;
@@ -386,7 +430,8 @@ public:
 
 			//dataspace
 			hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
-			dspace = new DataSpace (3,srcdims);
+			hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
+			dspace = new DataSpace (3,srcdims,srcdimsmax);
 
 			//dataset name
 			ostringstream osfn;
@@ -396,23 +441,28 @@ public:
 
 			//dataset
 			//chunked dataset if greater than max_chunked_images
-			if(nDimx > maxchunkedimages){
+			// always create chunked dataset as unlimited is only supported with chunked layout
 			DSetCreatPropList plist;
 			hsize_t chunk_dims[3] ={maxchunkedimages, nDimy, nDimz};
 			plist.setChunk(3, chunk_dims);
 			dset = new DataSet (fd->createDataSet(dsetname.c_str(), dtype, *dspace, plist));
-			}else
-				dset = new DataSet (fd->createDataSet(dsetname.c_str(), dtype, *dspace));
 
 			//create parameter datasets
 			hsize_t dims[1] = {nDimx};
-			dspace_para = new DataSpace (1,dims);
+			hsize_t dimsmax[1] = {H5S_UNLIMITED};
+			dspace_para = new DataSpace (1,dims,dimsmax);
+
+			// always create chunked dataset as unlimited is only supported with chunked layout
+			DSetCreatPropList paralist;
+			hsize_t chunkpara_dims[3] ={maxchunkedimages};
+			paralist.setChunk(1, chunkpara_dims);
+
 			for (int i = 0; i < NumberofParameters; ++i)
-				dset_para[i] = new DataSet(fd->createDataSet(ParameterNames[i], ParameterDataTypes[i], *dspace_para));
+				dset_para[i] = new DataSet(fd->createDataSet(ParameterNames[i], ParameterDataTypes[i], *dspace_para, paralist));
 		}
 		catch(Exception error){
 			cprintf(RED,"Error in creating HDF5 handles in object %d\n",ind);
-			error.printError();
+			error.printErrorStack();
 			fd->close();
 			return 1;
 		}
@@ -488,7 +538,7 @@ public:
 		hid_t vdsDataspace = H5Screate_simple(3, vdsdims ,NULL);
 		if (vdsDataspace < 0)
 			return CloseFileOnError(fd, string("Error in creating virtual dataspace in virtual file ") + virtualFileName + string("\n"));
-		hsize_t vdsdims_para[2] = {numf, numDety * numDetz};
+		hsize_t vdsdims_para[2] = {numf, (unsigned int)numDety * numDetz};
 		hid_t vdsDataspace_para = H5Screate_simple(2, vdsdims_para, NULL);
 		if (vdsDataspace_para < 0)
 			return CloseFileOnError(fd, string("Error in creating virtual dataspace (parameters) in virtual file ") + virtualFileName + string("\n"));
@@ -541,6 +591,14 @@ public:
 				string srcFileName = HDF5FileStatic::CreateFileName(fpath, fnameprefix, findex,
 						frindexenable, framesSaved, dindex, numunits, i);
 
+				// find relative path
+				string relative_srcFileName = srcFileName;
+				{
+					size_t i = srcFileName.rfind('/', srcFileName.length());
+					if (i != string::npos)
+						relative_srcFileName = (srcFileName.substr(i+1, srcFileName.length() - i));
+				}
+
 				//source dataset name
 				ostringstream osfn;
 				osfn << "/data";
@@ -549,23 +607,25 @@ public:
 
 				//source dataspace
 				hsize_t srcdims[3] = {nDimx, nDimy, nDimz};
-				hid_t srcDataspace = H5Screate_simple(3, srcdims, NULL);
+				hsize_t srcdimsmax[3] = {H5S_UNLIMITED, nDimy, nDimz};
+				hid_t srcDataspace = H5Screate_simple(3, srcdims, srcdimsmax);
 				if (srcDataspace < 0)
 					return CloseFileOnError(fd, string("Error in creating source dataspace in virtual file ") + virtualFileName + string("\n"));
 				hsize_t srcdims_para[1] = {nDimx};
-				hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, NULL);
+				hsize_t srcdimsmax_para[1] = {H5S_UNLIMITED};
+				hid_t srcDataspace_para = H5Screate_simple(1, srcdims_para, srcdimsmax_para);
 				if (srcDataspace_para < 0)
 					return CloseFileOnError(fd, string("Error in creating source dataspace (parameters) in virtual file ") + virtualFileName + string("\n"));
 
 				//mapping
-				if (H5Pset_virtual(dcpl, vdsDataspace, srcFileName.c_str(), srcDatasetName.c_str(), srcDataspace) < 0) {
+				if (H5Pset_virtual(dcpl, vdsDataspace, relative_srcFileName.c_str(), srcDatasetName.c_str(), srcDataspace) < 0) {
 					cprintf(RED,"could not set mapping for paramter 1\n");
 					error = true;
 					break;
 				}
 
 				for (int k = 0; k < NumberofParameters; ++k) {
-					if (H5Pset_virtual(dcpl_para[k], vdsDataspace_para, srcFileName.c_str(), ParameterNames[k], srcDataspace_para) < 0) {
+					if (H5Pset_virtual(dcpl_para[k], vdsDataspace_para, relative_srcFileName.c_str(), ParameterNames[k], srcDataspace_para) < 0) {
 						cprintf(RED,"could not set mapping for paramter %d\n", k);
 						error = true;
 						break;
@@ -587,7 +647,7 @@ public:
 			return CloseFileOnError(fd, string("Error in mapping files in virtual file ") + virtualFileName + string("\n"));
 
 		//dataset
-		string virtualDatasetName = string("/virtual_") + srcDataseName;
+		string virtualDatasetName = /*string("/virtual_") + */srcDataseName;
 		hid_t vdsdataset = H5Dcreate2 (fd, virtualDatasetName.c_str(), GetDataTypeinC(dataType), vdsDataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
 		if (vdsdataset < 0)
 			return CloseFileOnError(fd, string("Error in creating virutal dataset in virtual file ") + virtualFileName + string("\n"));
@@ -596,7 +656,7 @@ public:
 		//virtual parameter dataset
 		for (int i = 0; i < NumberofParameters; ++i) {
 			hid_t vdsdataset_para = H5Dcreate2 (fd,
-					(string("/virtual_") + string (ParameterNames[i])).c_str(),
+					(/*string("/virtual_") + */string (ParameterNames[i])).c_str(),
 					GetDataTypeinC(ParameterDataTypes[i]), vdsDataspace_para, H5P_DEFAULT, dcpl_para[i], H5P_DEFAULT);
 			if (vdsdataset_para < 0)
 				return CloseFileOnError(fd, string("Error in creating virutal dataset (parameters) in virtual file ") + virtualFileName + string("\n"));
@@ -697,7 +757,7 @@ public:
 			oldfd->close();
 		} catch(Exception error){
 			cprintf(RED,"Error in copying virtual files\n");
-			error.printError();
+			error.printErrorStack();
 			free(data_out);
 			oldfd->close();
 			newfd->close();
@@ -739,6 +799,14 @@ public:
 			return CloseFileOnError( vfd, string("Error in opening virtual file\n"));
 		}
 
+		// find relative path
+		string relative_virtualfname = virtualfname;
+		{
+			size_t i = virtualfname.rfind('/', virtualfname.length());
+			if (i != string::npos)
+				relative_virtualfname = (virtualfname.substr(i+1, virtualfname.length() - i));
+		}
+
 		//**data dataset**
 		hid_t vdset = H5Dopen2( vfd, virtualDatasetname.c_str(), H5P_DEFAULT);
 		if (vdset < 0) {
@@ -746,7 +814,7 @@ public:
 			return CloseFileOnError( vfd, string("Error in opening virtual data dataset\n"));
 		}
 		sprintf(linkname, "/entry/data/%s",virtualDatasetname.c_str());
-		if(H5Lcreate_external( virtualfname.c_str(), virtualDatasetname.c_str(),
+		if(H5Lcreate_external( relative_virtualfname.c_str(), virtualDatasetname.c_str(),
 										mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
 			H5Fclose(mfd); mfd = 0;
 			return CloseFileOnError( vfd, string("Error in creating link to data dataset\n"));
@@ -755,13 +823,13 @@ public:
 
 		//**paramter datasets**
 		for (int i = 0; i < NumberofParameters; ++i){
-			hid_t vdset_para = H5Dopen2( vfd, (string("/virtual_") + string (ParameterNames[i])).c_str(), H5P_DEFAULT);
+			hid_t vdset_para = H5Dopen2( vfd, (/*string("/virtual_") + */string (ParameterNames[i])).c_str(), H5P_DEFAULT);
 			if (vdset_para < 0) {
 				H5Fclose(mfd); mfd = 0;
 				return CloseFileOnError( vfd, string("Error in opening virtual parameter dataset to create link\n"));
 			}
-			sprintf(linkname, "/entry/data/%s",(string("/virtual_") + string (ParameterNames[i])).c_str());
-			if(H5Lcreate_external( virtualfname.c_str(), (string("/virtual_") + string (ParameterNames[i])).c_str(),
+			sprintf(linkname, "/entry/data/%s",(/*string("/virtual_") + */string (ParameterNames[i])).c_str());
+			if(H5Lcreate_external( relative_virtualfname.c_str(), (/*string("/virtual_") + */string (ParameterNames[i])).c_str(),
 					mfd, linkname, H5P_DEFAULT, H5P_DEFAULT) < 0) {
 				H5Fclose(mfd); mfd = 0;
 				return CloseFileOnError( vfd, string("Error in creating link to virtual parameter dataset\n"));

slsReceiverSoftware/include/gitInfoReceiver.h

@@ -1,6 +1,6 @@
 #define GITURL "git@github.com:slsdetectorgroup/slsDetectorPackage.git"
-#define GITREPUUID "b389402d647e939342dbb2c9317c688c0eb6b105"
-#define GITAUTH "Erik_Frojdh"
-#define GITREV 0x3458
-#define GITDATE 0x20180309
-#define GITBRANCH "3.1.0-rc"
+#define GITREPUUID "1b92b01a466aa1986b8198700274af75477a1e54"
+#define GITAUTH "Dhanya_Thattil"
+#define GITREV 0x3492
+#define GITDATE 0x20180817
+#define GITBRANCH "3.1.4"

slsReceiverSoftware/src/DataProcessor.cpp

@@ -282,9 +282,9 @@ void DataProcessor::CloseFiles() {
 		file->CloseAllFiles();
 }
 
-void DataProcessor::EndofAcquisition(uint64_t numf) {
+void DataProcessor::EndofAcquisition(bool anyPacketsCaught, uint64_t numf) {
 	if (file && file->GetFileType() == HDF5) {
-		file->EndofAcquisition(numf);
+		file->EndofAcquisition(anyPacketsCaught, numf);
 	}
 }
 

slsReceiverSoftware/src/HDF5File.cpp

@@ -38,7 +38,8 @@ HDF5File::HDF5File(int ind, uint32_t maxf, const uint32_t* ppf,
 		numFramesInFile(0),
 		numActualPacketsInFile(0),
 		numFilesinAcquisition(0),
-		dataspace_para(0)
+		dataspace_para(0),
+		extNumImages(0)
 {
 #ifdef VERBOSE
 	PrintMembers();
@@ -97,7 +98,7 @@ int HDF5File::CreateFile(uint64_t fnum) {
 	//first time
 	if(!fnum) UpdateDataType();
 
-	uint64_t framestosave = ((*numImages - fnum) > maxFramesPerFile) ? maxFramesPerFile : (*numImages-fnum);
+	uint64_t framestosave = ((extNumImages - fnum) > maxFramesPerFile) ? maxFramesPerFile : (extNumImages-fnum);
 	pthread_mutex_lock(&Mutex);
 	if (HDF5FileStatic::CreateDataFile(index, *overWriteEnable, currentFileName, *frameIndexEnable,
 			fnum, framestosave, nPixelsY, ((*dynamicRange==4) ? (nPixelsX/2) : nPixelsX),
@@ -111,9 +112,9 @@ int HDF5File::CreateFile(uint64_t fnum) {
 	if (dataspace == NULL)
 		cprintf(RED,"Got nothing!\n");
 
-	if(!silentMode)
+	if(!silentMode) {
 		FILE_LOG(logINFO) << *udpPortNumber << ": HDF5 File created: " << currentFileName;
-
+	}
 	return OK;
 }
 
@@ -145,6 +146,19 @@ int HDF5File::WriteToFile(char* buffer, int buffersize, uint64_t fnum, uint32_t
 	numFramesInFile++;
 	numActualPacketsInFile += nump;
 	pthread_mutex_lock(&Mutex);
+
+	// extend dataset (when receiver start followed by many status starts (jungfrau)))
+	if (fnum >= extNumImages) {
+		if (HDF5FileStatic::ExtendDataset(index, dataspace, dataset,
+				dataspace_para, dataset_para, *numImages) == OK) {
+			if (!silentMode) {
+				cprintf(BLUE,"%d Extending HDF5 dataset by %lu, Total x Dimension: %lu\n",
+					index, extNumImages, extNumImages + *numImages);
+			}
+			extNumImages += *numImages;
+		}
+	}
+
 	if (HDF5FileStatic::WriteDataFile(index, buffer + sizeof(sls_detector_header),
 			fnum%maxFramesPerFile, nPixelsY, ((*dynamicRange==4) ? (nPixelsX/2) : nPixelsX),
 			dataspace, dataset, datatype) == OK) {
@@ -163,18 +177,23 @@ int HDF5File::WriteToFile(char* buffer, int buffersize, uint64_t fnum, uint32_t
 }
 
 
+
+
+
 int HDF5File::CreateMasterFile(bool en, uint32_t size,
 		uint32_t nx, uint32_t ny, uint64_t at, uint64_t st, uint64_t ap) {
 
 	//beginning of every acquisition
 	numFramesInFile = 0;
 	numActualPacketsInFile = 0;
+	extNumImages = *numImages;
 
 	if (master && (*detIndex==0)) {
 		virtualfd = 0;
 		masterFileName = HDF5FileStatic::CreateMasterFileName(filePath, fileNamePrefix, *fileIndex);
-		if(!silentMode)
+		if(!silentMode){
 			FILE_LOG(logINFO) << "Master File: " << masterFileName;
+		}
 		pthread_mutex_lock(&Mutex);
 		int ret = HDF5FileStatic::CreateMasterDataFile(masterfd, masterFileName, *overWriteEnable,
 				*dynamicRange, en, size, nx, ny, *numImages, at, st, ap, HDF5_WRITER_VERSION);
@@ -185,11 +204,11 @@ int HDF5File::CreateMasterFile(bool en, uint32_t size,
 }
 
 
-void HDF5File::EndofAcquisition(uint64_t numf) {
+void HDF5File::EndofAcquisition(bool anyPacketsCaught, uint64_t numf) {
 	//not created before
-	if (!virtualfd) {
+	if (!virtualfd && anyPacketsCaught) {
 
-		//only one file and one sub image
+		//only one file and one sub image (link current file in master)
 		if (((numFilesinAcquisition == 1) && (numDetY*numDetX) == 1)) {
 			//dataset name
 			ostringstream osfn;
@@ -217,7 +236,7 @@ int HDF5File::CreateVirtualFile(uint64_t numf) {
 				virtualfd, masterFileName,
 				filePath, fileNamePrefix, *fileIndex, *frameIndexEnable,
 				*detIndex, *numUnitsPerDetector,
-				maxFramesPerFile, numf,
+				maxFramesPerFile, numf+1,
 				"data",	datatype,
 				numDetY, numDetX, nPixelsY, ((*dynamicRange==4) ? (nPixelsX/2) : nPixelsX),
 				HDF5_WRITER_VERSION);

slsReceiverSoftware/src/UDPBaseImplementation.cpp

@@ -290,7 +290,7 @@ void UDPBaseImplementation::setFilePath(const char c[]){
 		else
 			FILE_LOG(logERROR) << "FilePath does not exist: " << filePath;
 	}
-	FILE_LOG(logINFO) << "Info: File path: " << filePath;
+	FILE_LOG(logINFO) << "File path: " << filePath;
 }
 
 void UDPBaseImplementation::setFileIndex(const uint64_t i){

slsReceiverSoftware/src/UDPStandardImplementation.cpp

@@ -462,8 +462,9 @@ void UDPStandardImplementation::stopReceiver(){
 			if((*it)->GetMeasurementStartedFlag())
 				anycaught = true;
 		}
-		if (anycaught)
-			dataProcessor[0]->EndofAcquisition(maxIndexCaught); //to create virtual file
+
+		//to create virtual file & set files/acquisition to 0 (only hdf5 at the moment)
+		dataProcessor[0]->EndofAcquisition(anycaught, maxIndexCaught);
 	}
 
 	while(DataStreamer::GetRunningMask()){
@@ -480,7 +481,7 @@ void UDPStandardImplementation::stopReceiver(){
 			tot += dataProcessor[i]->GetNumFramesCaught();
 
 			uint64_t missingpackets = numberOfFrames*generalData->packetsPerFrame-listener[i]->GetPacketsCaught();
-			if (missingpackets) {
+			if ((int)missingpackets > 0) {
 				cprintf(RED, "\n[Port %d]\n",udpPortNum[i]);
 				cprintf(RED, "Missing Packets\t\t: %lld\n",(long long int)missingpackets);
 				cprintf(RED, "Complete Frames\t\t: %lld\n",(long long int)dataProcessor[i]->GetNumFramesCaught());
@@ -562,12 +563,15 @@ void UDPStandardImplementation::shutDownUDPSockets() {
 
 void UDPStandardImplementation::closeFiles() {
 	uint64_t maxIndexCaught = 0;
+	bool anycaught = false;
 	for (vector<DataProcessor*>::const_iterator it = dataProcessor.begin(); it != dataProcessor.end(); ++it) {
 		(*it)->CloseFiles();
 		maxIndexCaught = max(maxIndexCaught, (*it)->GetProcessedMeasurementIndex());
+		if((*it)->GetMeasurementStartedFlag())
+			anycaught = true;
 	}
-	if (maxIndexCaught)
-		dataProcessor[0]->EndofAcquisition(maxIndexCaught);
+	//to create virtual file & set files/acquisition to 0 (only hdf5 at the moment)
+	dataProcessor[0]->EndofAcquisition(anycaught, maxIndexCaught);
 }