Changes for page DAQ and data analysis

Last modified by sndueste on 2025/02/05 14:56
From version 16.1
edited by sndueste
on 2019/11/06 10:18
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To version 2.1
edited by sendels
on 2019/05/15 09:16
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1 -User overview
1 +Summary of DAQ / control options
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1 -XWiki.sndueste
1 +XWiki.sendels
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1 +\\
2 +
3 +\\
4 +
5 += Control and DAQ at FLASH (web version) =
6 +
1 1  Before starting a beamtime at FLASH the users have to consider several options regarding the control and data acquisition system where the users are supported by [[the controls group~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://photon-science.desy.de/facilities/flash/beamlines/daq_and_controls/index_eng.html||shape="rect"]].
2 2  
3 3  == Contents ==
... ... @@ -5,17 +5,18 @@
5 5  \\
6 6  
7 7  * Control and DAQ at FLASH (web version)
8 -** [[Overview>>doc:||anchor="Overview"]]
9 -** [[Things to consider before the beamtime>>doc:||anchor="Things to consider before the beamtime"]]
10 -** [[Beamline control and photon diagnostics>>doc:||anchor="Beamline control and photon diagnostics"]]
11 -** [[IT infrastructure>>doc:||anchor="IT infrastructure"]]
12 -** [[Data access>>doc:||anchor="Data access"]]
13 -** [[Online>>doc:||anchor="Online"]]
14 -** [[Data acquisition>>doc:||anchor="Data acquisition"]]
15 -** [[nearOnline>>doc:||anchor="nearOnline"]]
16 -*** [[.raw files>>doc:||anchor=".raw files"]]
17 -*** [[HDF5 files>>doc:||anchor="HDF5 files"]]
18 -** [[Offline>>doc:||anchor="Offline"]]
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 +***
23 +**** .raw files
24 +**** HDF5 files
25 +** Offline
19 19  
20 20  \\
21 21  
... ... @@ -25,55 +25,45 @@
25 25  
26 26  == Overview ==
27 27  
28 -[[image:attach:overview_flash_control_and_daq.png]]
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"]]
29 29  
30 -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:https://doocs-web.desy.de/index.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://jddd.desy.de/||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.
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.
31 31  
32 32  The data acquisition system (DAQ) collects beamline and experimental data and writes them to hard disk. All data are stored along with a time stamp and, in case of train specific data, along with a (pulse) train ID. There are several ways to access beamline and experimental data stored in the DAQ during or after the beamtime be it programmatically via DAQ access libraries or after data conversion to HDF5 format. While the data transport to the user's home institution is possible, DESY hosts high power computing resources which can be used for analysis.
33 33  
34 -[[Contents>>doc:||anchor="Contents"]]
35 -
36 36  == Things to consider before the beamtime ==
37 37  
38 -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>>attach:Before beamtime questionnaire.pdf]].
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"]].
39 39  
40 -[[Contents>>doc:||anchor="Contents"]]
41 -
42 42  == Beamline control and photon diagnostics ==
43 43  
44 44  Use existing jddd panel provided by FLASH or use the jddd editor to create a new panel according to the user's own needs.
45 45  
46 -The Java DOOCS Data Display (jddd) is a program to draw control system panels with an editor and to run the created drawings with real data. Two versions of the program are available. One is the jdddEditor to draw and test the drawings. The second one is a run-time version only, which does not allow to change a drawing. The jdddEditor offers reusable Java components like labels, buttons, plots, etc. to draw control system panels. The panel structure is stored in xml-format either to a local file system or to a subversion repository.
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"]]
47 47  
48 -[[ ~[~[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"]](% 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 -
50 50  \\
51 51  
52 52  (% class="wrapped" %)
53 53  |=(((
54 -[[DOOCS>>url:https://doocs-web.desy.de/index.html||shape="rect"]]
55 +[[DOOCS>>url:http://tesla.desy.de/doocs/index.html||title="DOOCS home" shape="rect"]]
55 55  )))|=(((
56 -[[jddd>>url:https://jddd.desy.de/||shape="rect"]]
57 +[[jddd>>url:http://ttfinfo2.desy.de/doocs/jddd/index.html||title="jddd home" shape="rect"]]
57 57  )))
58 58  
59 -[[Contents>>doc:||anchor="Contents"]]
60 -
61 61  == IT infrastructure ==
62 62  
63 -During a beamtime at FLASH we have two IT infrastructures each with different purpose. In the FLASH halls you have [[local machines>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.ComputingResourcesUserGuide.WebHome]] 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 +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"]].
64 64  
65 -[[image:attach:it-infrastructure2.png||height="400"]]
64 +[[image:url:http://hasfweb.desy.de/pub/Setup/Index/it-infrastructure2.png||alt="it-infrastructure2.png" width="800" height="393"]]
66 66  
67 -\\
66 +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"]].
67 +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.
68 68  
69 -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]].
70 -If the user is using his or her own DAQ system it is further possible to [[receive the trainId via network>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).How to read Train IDs at FLASH.WebHome]] for the purpose of synchronization.
71 -
72 72  \\
73 73  
74 74  (% class="wrapped" %)
75 75  |=(((
76 -[[local>>attach:jddd.jnlp]][[ machines>>attach:jddd.jnlp]]
73 +[[local machines>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide||shape="rect" class="twikiLink"]]
77 77  )))|=(((
78 78  (% class="content-wrapper" %)
79 79  (((
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80 80  [[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"]]
81 81  )))
82 82  )))|=(((
83 -[[doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).MTCA ADCs.WebHome]]
80 +[[MTCA ADCs>>url:http://hasfweb.desy.de/bin/view/Setup/MtcaAdc||shape="rect" class="twikiLink"]]
84 84  )))|=(((
85 -[[supported devices>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).DOOCS Device Support.WebHome]]
82 +[[supported devices>>url:http://hasfweb.desy.de/bin/view/Setup/DOOCS_supported_devices||shape="rect" class="twikiLink"]]
86 86  )))|=(((
87 87  (% class="content-wrapper" %)
88 88  (((
... ... @@ -89,22 +89,20 @@
89 89  [[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"]]
90 90  )))
91 91  )))|=(((
92 -[[trigger via MTCA>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).Trigger Howto.WebHome]]
89 +[[trigger via MTCA>>url:http://hasfweb.desy.de/bin/view/Setup/TriggerHowto||shape="rect" class="twikiLink"]]
93 93  )))|=(((
94 -[[trainId via network>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).How to read Train IDs at FLASH.WebHome]]
91 +[[trainId via network>>url:http://hasfweb.desy.de/bin/view/Setup/TrainID||shape="rect" class="twikiLink"]]
95 95  )))
96 96  
97 -[[Contents>>doc:||anchor="Contents"]]
94 +\\
98 98  
99 99  == Data access ==
100 100  
101 -\\
98 +[[image:url:http://hasfweb.desy.de/pub/Setup/Index/timescale_dataAccess.png||alt="timescale_dataAccess.png" width="1000" height="539"]]
102 102  
103 -[[image:attach:timescale_dataAccess.png||height="400"]]
100 +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.
101 +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.
104 104  
105 -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>>doc:FLASH.Online access to DOOCS properties]]) it is possible to request data directly from the DOOCS server by knowing the DOOCS address.
106 -As correlations of different physical properties are often required all data at FLASH are indexed by the [[trainID>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).How to read Train IDs at FLASH.WebHome]], which identify each of FLASH's pulse trains. The during a beamtime recorded data are stored via a Data Acquisition System ( [[DAQ>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).WebHome]]) which sort all events from the individual DOOCS server by trainID. When requested [[HDF files>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]] are created after the beamtime which includes the important data from [[the accelerator and its diagnostic>>doc:FLASHUSER.FLASH1 PhotDiag stream]] as well as the data created by the [[users>>doc:FLASHUSER.Configuring the user DAQs]]. 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.Near-Online data analysis]]. Reading synchronous data via an {{code language="none"}}online{{/code}} API is possible via a configurable DAQ middle layer server, the [[DAQmonitor>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).WebHome]], which feeds the correlated data back in the control system while it provides a ring buffer with 32 events in size.
107 -
108 108  \\
109 109  
110 110  (% class="wrapped" %)
... ... @@ -129,74 +129,57 @@
129 129  after the beamtime
130 130  )))
131 131  
132 -[[Contents>>doc:||anchor="Contents"]]
133 -
134 134  == Online ==
135 135  
136 -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.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Online data analysis.LabviewDOOCS (no longer supported).WebHome]]. For accessing the control system [[DOOCS addresses>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]] 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>>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.
137 137  
138 -A collection (Matlab [ [[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"]]] / [[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>>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.
139 139  
140 -[[Contents>>doc:||anchor="Contents"]]
141 -
142 142  == Data acquisition ==
143 143  
144 -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.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).How to read Train IDs at FLASH.WebHome]]. 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>>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.
145 145  
146 146  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.
147 147  
148 -While the DOOCS addresses are rather cryptic the [[HDF5 file>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]] 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>>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"]].
149 149  
150 150  \\
151 151  
152 -(% class="wrapped relative-table" %)
143 +(% class="wrapped" %)
153 153  |=(((
154 -[[DAQ introductions>>attach:Operator_training_DAQ_May_2016.pdf]]
145 +[[DAQ introduction>>url:http://hasfweb.desy.de/pub/Setup/DAQmain/Operator_training_DAQ_May_2016.pdf||shape="rect"]]
155 155  )))|=(((
156 -[[FLASH1 PBD>>doc:FLASHUSER.FLASH1 PhotDiag stream]]
147 +[[FLASH1 PBD>>url:http://hasfweb.desy.de/bin/view/Setup/DAQPbdDescription||shape="rect" class="twikiLink"]]
157 157  )))|=(((
158 -[[FLASH2 PBD>>doc:FLASHUSER.FLASH2 PhotDiag stream]]
149 +[[FLASH2 PBD>>url:http://hasfweb.desy.de/bin/view/Setup/FL2PhotDiagDataStream||shape="rect" class="twikiLink"]]
159 159  )))|=(((
160 -[[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]]
151 +[[User DAQs>>url:http://hasfweb.desy.de/bin/view/Setup/DAQjddd||shape="rect" class="twikiLink"]]
161 161  )))|=(((
162 -[[User DAQs subsytems>>doc:FLASHUSER.Configuring the user DAQs]]
153 +[[User DAQs subsytems>>url:http://hasfweb.desy.de/bin/view/Setup/DAQExp2Description||shape="rect" class="twikiLink"]]
163 163  )))|=(((
164 -[[HDF5 files>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]]
155 +[[HDF5 files>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main||shape="rect" class="twikiLink"]]
165 165  )))
166 166  
167 -[[Contents>>doc:||anchor="Contents"]]
168 -
169 169  == nearOnline ==
170 170  
171 171  ==== .raw files ====
172 172  
173 -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:FLASH.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]].
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>>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"]].
174 174  
175 175  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.
176 176  
177 177  ==== HDF5 files ====
178 178  
179 -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.Near-Online data analysis]] an API which handles a lot of the occurring difficulties as knowing the file or DAQ instances. The [[BeamtimeDaqAccess>>doc:FLASHUSER.Near-Online data analysis]] 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>>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.
180 180  
181 -[[Contents>>doc:||anchor="Contents"]]
182 -
183 183  == Offline ==
184 184  
185 -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.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]] 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.
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>>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.
186 186  
187 187  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.
188 188  
189 -[[Contents>>doc:||anchor="Contents"]]
190 -
191 191  \\
192 192  
193 193  ----
194 194  
195 -**//
196 -//**
197 -
198 -\\
199 -
200 -\\
201 -
202 -\\
180 +**//NOTE~://** Content below the STOPPUBLISH variable is not published. Use this space as a scrap area.