Changes for page DAQ and data analysis

Last modified by sndueste on 2025/02/05 14:56
From version 1.1
edited by sendels
on 2019/05/15 09:06
Change comment: There is no comment for this version
To version 7.1
edited by sendels
on 2019/05/16 08:43
Change comment: There is no comment for this version

Summary

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Content
... ... @@ -10,19 +10,19 @@
10 10  
11 11  \\
12 12  
13 -* [[Control and DAQ at FLASH (web version)>>url:http://hasfweb.desy.de/bin/view/Setup/Index#Control_and_DAQ_at_FLASH_web_ver||shape="rect"]]
14 -** [[Overview>>url:http://hasfweb.desy.de/bin/view/Setup/Index#Overview||shape="rect"]]
15 -** [[Things to consider before the beamtime>>url:http://hasfweb.desy.de/bin/view/Setup/Index#Things_to_consider_before_the_be||shape="rect"]]
16 -** [[Beamline control and photon diagnostics>>url:http://hasfweb.desy.de/bin/view/Setup/Index#Beamline_control_and_photon_diag||shape="rect"]]
17 -** [[IT infrastructure>>url:http://hasfweb.desy.de/bin/view/Setup/Index#IT_infrastructure||shape="rect"]]
18 -** [[Data access>>url:http://hasfweb.desy.de/bin/view/Setup/Index#Data_access||shape="rect"]]
19 -** [[Online>>url:http://hasfweb.desy.de/bin/view/Setup/Index#Online||shape="rect"]]
20 -** [[Data acquisition>>url:http://hasfweb.desy.de/bin/view/Setup/Index#Data_acquisition||shape="rect"]]
21 -** [[nearOnline>>url:http://hasfweb.desy.de/bin/view/Setup/Index#nearOnline||shape="rect"]]
13 +* Control and DAQ at FLASH (web version)
14 +** Overview
15 +** Things to consider before the beamtime
16 +** Beamline control and photon diagnostics
17 +** IT infrastructure
18 +** Data access
19 +** Online
20 +** Data acquisition
21 +** nearOnline
22 22  ***
23 -**** [[.raw files>>url:http://hasfweb.desy.de/bin/view/Setup/Index#raw_files||shape="rect"]]
24 -**** [[HDF5 files>>url:http://hasfweb.desy.de/bin/view/Setup/Index#HDF5_files||shape="rect"]]
25 -** [[Offline>>url:http://hasfweb.desy.de/bin/view/Setup/Index#Offline||shape="rect"]]
23 +**** .raw files
24 +**** HDF5 files
25 +** Offline
26 26  
27 27  \\
28 28  
... ... @@ -32,7 +32,7 @@
32 32  
33 33  == Overview ==
34 34  
35 -[[image:url:http://hasfweb.desy.de/pub/Setup/Index/overview_flash_control_and_daq.png||alt="overview_flash_control_and_daq.png" width="748" title="overview_flash_control_and_daq.png" height="823"]]
35 +[[image:url:http://hasfweb.desy.de/pub/Setup/Index/overview_flash_control_and_daq.png||alt="overview_flash_control_and_daq.png" width="748" height="823"]]
36 36  
37 37  The FLASH accelerator, beamlines and experiments are using the Distributed Object Oriented Control System ( [[DOOCS~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://tesla.desy.de/doocs/doocs.html||shape="rect"]]). Beamline and experiment devices are mainly operated via graphical user interfaces created with the Java DOOCS Data Display ( [[jddd~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://doocs-web.desy.de/access.html||shape="rect"]]) by the FLASH team or the users themself. Further it is provided a [[DOOCS client API~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://ttfinfo.desy.de/DOOCSWiki/Wiki.jsp?page=DOOCS%20Wiki||shape="rect"]] in Java, Python, Matlab, C or C++ to the users to write own software for data access, online data or device control. User-provided devices can be run in parallel or can be implemented in DOOCS. For each beamline and accelerator is a dedicated [[electronic logbook~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://tesla.desy.de/ttf_apps/showElogs.jsp||shape="rect"]] available in which jddd and other software can print directly.
38 38  
... ... @@ -40,16 +40,17 @@
40 40  
41 41  == Things to consider before the beamtime ==
42 42  
43 -In consultation with the user's local contact the user should check our [[beamtime preparation checklist>>url:http://hasfweb.desy.de/bin/view/Setup/BeforeBeamtimeChecklist||shape="rect" class="twikiLink"]] and fill in the [[beamtime preparation questionnaire>>url:http://hasfweb.desy.de/pub/Setup/ITManuals/Before_beamtime_questionnaire.pdf||shape="rect"]].
43 +In consultation with the user's local contact the user should check our [[beamtime preparation checklist>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Before beamtime Checklist.WebHome]] and fill in the [[beamtime preparation questionnaire>>url:http://hasfweb.desy.de/pub/Setup/ITManuals/Before_beamtime_questionnaire.pdf||shape="rect"]].
44 44  
45 45  == Beamline control and photon diagnostics ==
46 46  
47 47  Use existing jddd panel provided by FLASH or use the jddd editor to create a new panel according to the user's own needs.
48 48  
49 -[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/Index/jddd_logo.png~|~|alt="jddd Photon Beamline Controls" width="125" title="jddd Photon Beamline Controls" height="80"~]~]~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://ttfinfo2.desy.de/common/applications/jddd_xml/run_jnlp.jsp?run=true&file=/svn/FLASH/Hasylab/Photons_beamline_control_main.xml||shape="rect"]][[~[~[image:url:http://hasfweb.desy.de/pub/Setup/Index/jdddEditor.png~|~|alt="jdddEditor.png" width="125"~]~]>>url:http://ttfinfo2.desy.de/common/applications/jddd.jnlp?run=true||title="jddd editor" shape="rect"]](% class="twikiNewLink" %)[[url:http://hasfweb.desy.de/bin/edit/Ttfinfo2/desy/de/common/applications/jddd/Jnlp?topicparent=Setup.Index;nowysiwyg=0||rel="nofollow" shape="rect"]]
49 +[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/Index/jddd_logo.png~|~|alt="jddd Photon Beamline Controls" width="125" height="80"~]~]~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://ttfinfo2.desy.de/common/applications/jddd_xml/run_jnlp.jsp?run=true&file=/svn/FLASH/Hasylab/Photons_beamline_control_main.xml||shape="rect"]][[~[~[image:url:http://hasfweb.desy.de/pub/Setup/Index/jdddEditor.png~|~|alt="jdddEditor.png" width="125"~]~]>>url:http://ttfinfo2.desy.de/common/applications/jddd.jnlp?run=true||title="jddd editor" shape="rect"]](% class="twikiNewLink" %)[[url:http://hasfweb.desy.de/bin/edit/Ttfinfo2/desy/de/common/applications/jddd/Jnlp?topicparent=Setup.Index;nowysiwyg=0||rel="nofollow" shape="rect"]]
50 50  
51 51  \\
52 52  
53 +(% class="wrapped" %)
53 53  |=(((
54 54  [[DOOCS>>url:http://tesla.desy.de/doocs/index.html||title="DOOCS home" shape="rect"]]
55 55  )))|=(((
... ... @@ -60,23 +60,30 @@
60 60  
61 61  During a beamtime at FLASH we have two IT infrastructures each with different purpose. In the FLASH halls you have [[local machines>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide||shape="rect" class="twikiLink"]] which are used with functional accounts and they have access to the [[beamline files-system~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3/Directory+Structure||shape="rect"]] for your current experiment. For more demanding task we could also provide workstations which can be dedicated to a single user experiment. For offline and nearOnline analysis the [[Maxwell cluster~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/IS/Maxwell||shape="rect"]] for high performance computing is available. On the Maxwell cluster you have to work with personal accounts as this regulates data access to the [[core file-system~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3/Directory+Structure||shape="rect"]].
62 62  
63 -[[image:url:http://hasfweb.desy.de/pub/Setup/Index/it-infrastructure2.png||alt="it-infrastructure2.png" width="800" title="it-infrastructure2.png" height="393"]]
64 +[[image:url:http://hasfweb.desy.de/pub/Setup/Index/it-infrastructure2.png||alt="it-infrastructure2.png" width="800" height="393"]]
64 64  
65 -The FLASH control & DAQ system supports [[several devices>>url:http://hasfweb.desy.de/bin/view/Setup/DOOCS_supported_devices||shape="rect" class="twikiLink"]] and at each beamline are [[MTCA ADCs>>url:http://hasfweb.desy.de/bin/view/Setup/MtcaAdc||shape="rect" class="twikiLink"]] available. With the MTCA technology it is possible to [[synchronize own devices in respect to the FEL>>url:http://hasfweb.desy.de/bin/view/Setup/TriggerHowto||shape="rect" class="twikiLink"]].
66 -If the user is using his or her own DAQ system it is further possible to [[receive the trainId via network>>url:http://hasfweb.desy.de/bin/view/Setup/TrainID||shape="rect" class="twikiLink"]] for the purpose of synchronization.
66 +The FLASH control & DAQ system supports [[several devices>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).DOOCS Device Support.WebHome]] and at each beamline are [[doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).MTCA ADCs.WebHome]] available. With the MTCA technology it is possible to [[synchronize own devices in respect to the FEL>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).Trigger Howto.WebHome]].
67 +If the user is using his or her own DAQ system it is further possible to [[receive the trainId via network>>doc:FLASHUSER.TrainID]] for the purpose of synchronization.
67 67  
68 68  \\
69 69  
71 +(% class="wrapped" %)
70 70  |=(((
71 71  [[local machines>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide||shape="rect" class="twikiLink"]]
72 72  )))|=(((
75 +(% class="content-wrapper" %)
76 +(((
73 73  [[Maxwell cluster~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/IS/Maxwell||shape="rect"]]
78 +)))
74 74  )))|=(((
75 75  [[MTCA ADCs>>url:http://hasfweb.desy.de/bin/view/Setup/MtcaAdc||shape="rect" class="twikiLink"]]
76 76  )))|=(((
77 77  [[supported devices>>url:http://hasfweb.desy.de/bin/view/Setup/DOOCS_supported_devices||shape="rect" class="twikiLink"]]
78 78  )))|=(((
84 +(% class="content-wrapper" %)
85 +(((
79 79  [[supported cameras~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://ttfinfo.desy.de/FLASHWiki/Wiki.jsp?page=Camera%20server||shape="rect"]]
87 +)))
80 80  )))|=(((
81 81  [[trigger via MTCA>>url:http://hasfweb.desy.de/bin/view/Setup/TriggerHowto||shape="rect" class="twikiLink"]]
82 82  )))|=(((
... ... @@ -87,13 +87,14 @@
87 87  
88 88  == Data access ==
89 89  
90 -[[image:url:http://hasfweb.desy.de/pub/Setup/Index/timescale_dataAccess.png||alt="timescale_dataAccess.png" width="1000" title="timescale_dataAccess.png" height="539"]]
98 +[[image:url:http://hasfweb.desy.de/pub/Setup/Index/timescale_dataAccess.png||alt="timescale_dataAccess.png" width="1000" height="539"]]
91 91  
92 92  At the Free-electron Laser Hamburg ( [[FLASH~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://flash.desy.de/||shape="rect"]]) we use the Distributed Object Oriented Control System ( [[DOOCS~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://tesla.desy.de/doocs/doocs.html||shape="rect"]]). Devices are implemented via DOOCS server and via an API ( [[ONLINE>>url:http://hasfweb.desy.de/bin/view/Setup/OnlineAPIs||shape="rect" class="twikiLink"]]) it is possible to request data directly from the DOOCS server by knowing the DOOCS address.
93 -As correlations of different physical properties are often required all data at FLASH are indexed by the [[trainID>>url:http://hasfweb.desy.de/bin/view/Setup/TrainID||shape="rect" class="twikiLink"]], which identify each of FLASH's pulse trains. The during a beamtime recorded data are stored via a Data Acquisition System ( [[DAQ>>url:http://hasfweb.desy.de/bin/view/Setup/DAQmain||shape="rect" class="twikiLink"]]) which sort all events from the individual DOOCS server by trainID. When requested [[HDF files>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main||shape="rect" class="twikiLink"]] are created after the beamtime which includes the important data from [[the accelerator and its diagnostic>>url:http://hasfweb.desy.de/bin/view/Setup/DAQPbdDescription||shape="rect" class="twikiLink"]] as well as the data created by the [[users>>url:http://hasfweb.desy.de/bin/view/Setup/DAQExp2Description||shape="rect" class="twikiLink"]]. This time scale we define as {{code language="none"}}offline{{/code}} as the HDF files are converted after the beamtime is over. For synchronous data during an experiment it is possible to create shorter HDF slices via a {{code language="none"}}nearOnline{{/code}} converter within a few minutes. For working with this partially incomplete HDF slices we provide an API called [[BeamtimeDaqAccess>>url:http://hasfweb.desy.de/bin/view/Setup/BeamtimeDaqAccess||shape="rect" class="twikiLink"]]. Reading synchronous data via an {{code language="none"}}online{{/code}} API is possible via a configurable DAQ middle layer server, the [[DAQmonitor>>url:http://hasfweb.desy.de/bin/view/Setup/ConfigureDAQmonitor||shape="rect" class="twikiLink"]], which feeds the correlated data back in the control system while it provides a ring buffer with 32 events in size.
101 +As correlations of different physical properties are often required all data at FLASH are indexed by the [[trainID>>doc:FLASHUSER.TrainID]], which identify each of FLASH's pulse trains. The during a beamtime recorded data are stored via a Data Acquisition System ( [[DAQ>>doc:FLASHUSER.Information about the FLASH DAQ system]]) which sort all events from the individual DOOCS server by trainID. When requested [[HDF files>>doc:FLASHUSER.Information about the FLASH HDF5 structure]] are created after the beamtime which includes the important data from [[the accelerator and its diagnostic>>doc:FLASHUSER.PBD DAQ]] as well as the data created by the [[users>>doc:FLASHUSER.Description of the Properties in the FLASH1_USER1, 2 and 3 for FLASH1 Users]]. This time scale we define as {{code language="none"}}offline{{/code}} as the HDF files are converted after the beamtime is over. For synchronous data during an experiment it is possible to create shorter HDF slices via a {{code language="none"}}nearOnline{{/code}} converter within a few minutes. For working with this partially incomplete HDF slices we provide an API called [[BeamtimeDaqAccess>>doc:FLASHUSER.Beamtime DAQ Access]]. Reading synchronous data via an {{code language="none"}}online{{/code}} API is possible via a configurable DAQ middle layer server, the [[DAQmonitor>>doc:AIDA2020ESST.DAQ Monitor]], which feeds the correlated data back in the control system while it provides a ring buffer with 32 events in size.
94 94  
95 95  \\
96 96  
105 +(% class="wrapped" %)
97 97  |(((
98 98  online
99 99  )))|(((
... ... @@ -117,32 +117,33 @@
117 117  
118 118  == Online ==
119 119  
120 -To monitor individual parameters online, e.g. ADCs or cameras, the use of jddd is recommended. For more complex tasks the users can use the DOOCS client API for [[Matlab>>url:http://hasfweb.desy.de/bin/view/Setup/MatlabDOOCS||shape="rect" class="twikiLink"]], [[Python>>url:http://hasfweb.desy.de/bin/view/Setup/PythonDOOCS||shape="rect" class="twikiLink"]] and [[Labview>>url:http://hasfweb.desy.de/bin/view/Setup/LabviewDOOCS||shape="rect" class="twikiLink"]]. For accessing the control system [[DOOCS addresses>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main||shape="rect" class="twikiLink"]] are required.
129 +To monitor individual parameters online, e.g. ADCs or cameras, the use of jddd is recommended. For more complex tasks the users can use the DOOCS client API for [[Matlab>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Online data analysis.MatlabDOOCS.WebHome]], [[Python>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Online data analysis.PythonDOOCS.WebHome]] and [[Labview>>doc:FLASHUSER.How to read and write DOOCS properties with LABVIEW]]. For accessing the control system [[DOOCS addresses>>doc:FLASHUSER.Information about the FLASH HDF5 structure]] are required.
121 121  
122 -A collection (Matlab [ [[scan tool>>url:http://hasfweb.desy.de/bin/view/Setup/MatlabScanTools||shape="rect" class="twikiLink"]] , [[TOF & camera GUIs~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://stash.desy.de/projects/FSFL/repos/matlab-guis/browse||shape="rect"]], [[others>>url:http://hasfweb.desy.de/bin/view/Setup/UserCodeCollection||shape="rect" class="twikiLink"]]] / [[Juypter notebooks~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://stash.desy.de/projects/FSFL/repos/jupyter-notebook/browse||shape="rect"]]) for common use cases is available.
131 +A collection (Matlab [ [[scan tool>>doc:FLASHUSER.Matlab Scantools]] , [[TOF & camera GUIs~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://stash.desy.de/projects/FSFL/repos/matlab-guis/browse||shape="rect"]], [[others>>doc:FLASHUSER.Collection of user codes]]] / [[Juypter notebooks~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://stash.desy.de/projects/FSFL/repos/jupyter-notebook/browse||shape="rect"]]) for common use cases is available.
123 123  
124 124  == Data acquisition ==
125 125  
126 -Relevant machine data, e.g. pulse energy or arrival time, are are saved in the FLASH Photon diagnostics DAQ (PBD) while experiment related parameter are saved on demand in the FLASH [[User DAQs>>url:http://hasfweb.desy.de/bin/view/Setup/DAQjddd||shape="rect" class="twikiLink"]]. In addition it is disk space availabe for devices and paramter outside the FLASH DAQ, which can be [[synchronized via Ethernet connection>>url:http://hasfweb.desy.de/bin/view/Setup/TrainID||shape="rect" class="twikiLink"]]. The for the beamtime provided storage space, the [[spectrum scale~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3/Architecture||shape="rect"]] formerly known as ASAP3/GPFS, is access regulated via [[DOOR~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://door.desy.de/door/index.php||shape="rect"]] and only registered participants have access.
135 +Relevant machine data, e.g. pulse energy or arrival time, are are saved in the FLASH Photon diagnostics DAQ (PBD) while experiment related parameter are saved on demand in the FLASH [[User DAQs>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).How to save data in the User DAQ.WebHome]]. In addition it is disk space availabe for devices and paramter outside the FLASH DAQ, which can be [[ synchronized via Ethernet connection>>doc:FLASHUSER.TrainID]]. The for the beamtime provided storage space, the [[spectrum scale~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3/Architecture||shape="rect"]] formerly known as ASAP3/GPFS, is access regulated via [[DOOR~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://door.desy.de/door/index.php||shape="rect"]] and only registered participants have access.
127 127  
128 128  The FLASH DAQ system records the data in binary .raw files. On request the data will also be available in the HDF5 format after a conversion during or after the beamtime. Incoming data is collected, sorted and saved into .raw files in chunks of 60 MB to 1 GB which corresponds to tens of seconds up to several minutes. The HDF5 files can be created nearOnline or Offline. In the nearOnline conversion every individual .raw files will be converted to a single HDF5 file to provide the fastest access possible. After the beamtime it is possible to get a HDF5 file per DAQ run which is very convenient as it contains the merged data of the User DAQ and the PBD DAQ.
129 129  
130 -While the DOOCS addresses are rather cryptic the [[HDF5 file>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main||shape="rect" class="twikiLink"]] is structured based on the actual location and function of the devices. A complete list is available in [[DESY's Repository~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://stash.desy.de/projects/CS/repos/pah/browse/src/camp/data/channel2HdfName.dat||shape="rect"]].
139 +While the DOOCS addresses are rather cryptic the [[HDF5 file>>doc:FLASHUSER.Information about the FLASH HDF5 structure]] is structured based on the actual location and function of the devices. A complete list is available in [[DESY's Repository~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://stash.desy.de/projects/CS/repos/pah/browse/src/camp/data/channel2HdfName.dat||shape="rect"]].
131 131  
132 132  \\
133 133  
143 +(% class="wrapped" %)
134 134  |=(((
135 135  [[DAQ introduction>>url:http://hasfweb.desy.de/pub/Setup/DAQmain/Operator_training_DAQ_May_2016.pdf||shape="rect"]]
136 136  )))|=(((
137 -[[FLASH1 PBD>>url:http://hasfweb.desy.de/bin/view/Setup/DAQPbdDescription||shape="rect" class="twikiLink"]]
147 +[[FLASH1 PBD>>doc:FLASHUSER.PBD DAQ]]
138 138  )))|=(((
139 -[[FLASH2 PBD>>url:http://hasfweb.desy.de/bin/view/Setup/FL2PhotDiagDataStream||shape="rect" class="twikiLink"]]
149 +[[FLASH2 PBD>>doc:FLASHUSER.FL2PhotDiag stream (status Feb 2017)]]
140 140  )))|=(((
141 -[[User DAQs>>url:http://hasfweb.desy.de/bin/view/Setup/DAQjddd||shape="rect" class="twikiLink"]]
151 +[[User DAQs>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).How to save data in the User DAQ.WebHome]]
142 142  )))|=(((
143 -[[User DAQs subsytems>>url:http://hasfweb.desy.de/bin/view/Setup/DAQExp2Description||shape="rect" class="twikiLink"]]
153 +[[User DAQs subsytems>>doc:FLASHUSER.Description of the Properties in the FLASH1_USER1, 2 and 3 for FLASH1 Users]]
144 144  )))|=(((
145 -[[HDF5 files>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main||shape="rect" class="twikiLink"]]
155 +[[HDF5 files>>doc:FLASHUSER.Information about the FLASH HDF5 structure]]
146 146  )))
147 147  
148 148  == nearOnline ==
... ... @@ -149,17 +149,17 @@
149 149  
150 150  ==== .raw files ====
151 151  
152 -The .raw files are only accessible from certain computers within the DESY network and in generell it is not recommended to use them directly. For checking the file content and doing simple analysis, e.g. histogram, line outs, we provide the [[DAQdataGUI>>url:http://hasfweb.desy.de/bin/view/Setup/DAQRootGui#How_to_Use_the_FLASH_DAQ_Data_GU||shape="rect" class="twikiAnchorLink"]]. If the user already have very precise knowledge of the desired parameters and it's types it is possible [[to read with Matlab from the files directly>>url:http://hasfweb.desy.de/bin/view/Setup/DAQMatlabAccessExamples||shape="rect" class="twikiLink"]].
162 +The .raw files are only accessible from certain computers within the DESY network and in generell it is not recommended to use them directly. For checking the file content and doing simple analysis, e.g. histogram, line outs, we provide the [[DAQdataGUI>>doc:FLASHUSER.How to get the data out of the DAQ]]. If the user already have very precise knowledge of the desired parameters and it's types it is possible [[to read with Matlab from the files directly>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).For experts\: many ways to get Data from the DAQ.How to Access the DAQ Using Matlab.WebHome]].
153 153  
154 154  FLASH's DAQ .raw files are saved locally and with a time delay of a few minutes backupped via tape ( [[dCache~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3/Managing+data+taken+before+April+2015||shape="rect"]]) by the DESY central IT.
155 155  
156 156  ==== HDF5 files ====
157 157  
158 -As the .raw files are highly optimized for writing speed there are some issues which have to be taken care of which are also present in the nearOnline HDF5 files (e.g. missing/doubled events). For this we provide with [[BeamtimeDaqAccess>>url:http://hasfweb.desy.de/bin/view/Setup/BeamtimeDaqAccess||shape="rect" class="twikiLink"]] an API which handles a lot of the occurring difficulties as knowing the file or DAQ instances. The [[BeamtimeDaqAccess>>url:http://hasfweb.desy.de/bin/view/Setup/BeamtimeDaqAccess||shape="rect" class="twikiLink"]] library is written in Python, but a Matlab wrapper is available.
168 +As the .raw files are highly optimized for writing speed there are some issues which have to be taken care of which are also present in the nearOnline HDF5 files (e.g. missing/doubled events). For this we provide with [[BeamtimeDaqAccess>>doc:FLASHUSER.Beamtime DAQ Access]] an API which handles a lot of the occurring difficulties as knowing the file or DAQ instances. The [[BeamtimeDaqAccess>>doc:FLASHUSER.Beamtime DAQ Access]] library is written in Python, but a Matlab wrapper is available.
159 159  
160 160  == Offline ==
161 161  
162 -The offline HDF5 files containing complete DAQ runs will be put after the beamtime on the spectrum scale file system. Access is granted from the within the DESY network for beamtime participants or from the outside via [[Gamma portal~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3/The+Gamma+Portal||shape="rect"]]. HDF-by-run files can processed with common tools, e.g. with [[Matlab>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main#Samples_how_to_read_HDF5_with_Ma||shape="rect" class="twikiAnchorLink"]] or [[Python>>url:http://hasfweb.desy.de/bin/view/Setup/FlashH5||shape="rect" class="twikiLink"]], as during the conversion a lot of discrepancies have been resolved. As .raw files are rarely used for analysis they are saved on the FLASH DAQ servers and will only be put on the spectrum scale file system on special request.
172 +The offline HDF5 files containing complete DAQ runs will be put after the beamtime on the spectrum scale file system. Access is granted from the within the DESY network for beamtime participants or from the outside via [[Gamma portal~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3/The+Gamma+Portal||shape="rect"]]. HDF-by-run files can processed with common tools, e.g. with [[Matlab>>doc:FLASHUSER.Information about the FLASH HDF5 structure]] or [[Python>>doc:FLASHUSER.FLASHH5 for easier access of FLASH's HDF5 files]], as during the conversion a lot of discrepancies have been resolved. As .raw files are rarely used for analysis they are saved on the FLASH DAQ servers and will only be put on the spectrum scale file system on special request.
163 163  
164 164  The spectrum scale file system contains the [[substructure~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://confluence.desy.de/display/ASAP3/Directory+Structure||shape="rect"]]: {{code language="none"}}raw{{/code}}, {{code language="none"}}processed{{/code}}, {{code language="none"}}shared{{/code}} and {{code language="none"}}scratch{{/code}}. The (% class="WYSIWYG_TT" %)raw (%%)folder contains the data recorded by the experiment (user data and HDF5) and will be set read only shortly after the beamtime is over. {{code language="none"}}Processed{{/code}} is typically used to store processed data and analysis software. Both folder are backupped by the spectrum scale file system.
165 165