Changes for page DAQ and data analysis

Last modified by sndueste on 2025/02/05 14:56
From version 11.1
edited by sendels
on 2019/08/06 14:29
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To version 7.1
edited by sendels
on 2019/05/16 08:43
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Summary

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1 -User overview
1 +Summary of DAQ / control options
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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  
... ... @@ -25,25 +25,21 @@
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 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: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 -[[ ~[~[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"]]
47 47  
48 48  \\
49 49  
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54 54  [[jddd>>url:http://ttfinfo2.desy.de/doocs/jddd/index.html||title="jddd home" shape="rect"]]
55 55  )))
56 56  
57 -[[Contents>>doc:||anchor="Contents"]]
58 -
59 59  == IT infrastructure ==
60 60  
61 -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"]].
62 62  
63 -[[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"]]
64 64  
65 -\\
66 -
67 67  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]].
68 -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.
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.
69 69  
70 70  \\
71 71  
72 72  (% class="wrapped" %)
73 73  |=(((
74 -[[local>>attach:jddd.jnlp]][[ machines>>attach:jddd.jnlp]]
73 +[[local machines>>url:http://hasfweb.desy.de/bin/view/Setup/ComputingResourcesUserGuide||shape="rect" class="twikiLink"]]
75 75  )))|=(((
76 76  (% class="content-wrapper" %)
77 77  (((
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78 78  [[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"]]
79 79  )))
80 80  )))|=(((
81 -[[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"]]
82 82  )))|=(((
83 -[[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"]]
84 84  )))|=(((
85 85  (% class="content-wrapper" %)
86 86  (((
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87 87  [[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"]]
88 88  )))
89 89  )))|=(((
90 -[[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"]]
91 91  )))|=(((
92 -[[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"]]
93 93  )))
94 94  
95 -[[Contents>>doc:||anchor="Contents"]]
94 +\\
96 96  
97 97  == Data access ==
98 98  
99 -\\
98 +[[image:url:http://hasfweb.desy.de/pub/Setup/Index/timescale_dataAccess.png||alt="timescale_dataAccess.png" width="1000" height="539"]]
100 100  
101 -[[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>>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.
102 102  
103 -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:FLASHUSER.Online access to DOOCS properties]]) it is possible to request data directly from the DOOCS server by knowing the DOOCS address.
104 -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:AIDA2020ESST.DAQ Monitor]], which feeds the correlated data back in the control system while it provides a ring buffer with 32 events in size.
105 -
106 106  \\
107 107  
108 108  (% class="wrapped" %)
... ... @@ -127,43 +127,37 @@
127 127  after the beamtime
128 128  )))
129 129  
130 -[[Contents>>doc:||anchor="Contents"]]
131 -
132 132  == Online ==
133 133  
134 -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>>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.
135 135  
136 136  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.
137 137  
138 -[[Contents>>doc:||anchor="Contents"]]
139 -
140 140  == Data acquisition ==
141 141  
142 -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>>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.
143 143  
144 144  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.
145 145  
146 -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>>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"]].
147 147  
148 148  \\
149 149  
150 -(% class="wrapped relative-table" %)
143 +(% class="wrapped" %)
151 151  |=(((
152 -[[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"]]
153 153  )))|=(((
154 -[[FLASH1 PBD>>doc:FLASHUSER.FLASH1 PhotDiag stream]]
147 +[[FLASH1 PBD>>doc:FLASHUSER.PBD DAQ]]
155 155  )))|=(((
156 -[[FLASH2 PBD>>doc:FLASHUSER.FLASH2 PhotDiag stream]]
149 +[[FLASH2 PBD>>doc:FLASHUSER.FL2PhotDiag stream (status Feb 2017)]]
157 157  )))|=(((
158 158  [[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]]
159 159  )))|=(((
160 -[[User DAQs subsytems>>doc:FLASHUSER.Configuring the user DAQs]]
153 +[[User DAQs subsytems>>doc:FLASHUSER.Description of the Properties in the FLASH1_USER1, 2 and 3 for FLASH1 Users]]
161 161  )))|=(((
162 -[[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>>doc:FLASHUSER.Information about the FLASH HDF5 structure]]
163 163  )))
164 164  
165 -[[Contents>>doc:||anchor="Contents"]]
166 -
167 167  == nearOnline ==
168 168  
169 169  ==== .raw files ====
... ... @@ -174,27 +174,16 @@
174 174  
175 175  ==== HDF5 files ====
176 176  
177 -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>>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.
178 178  
179 -[[Contents>>doc:||anchor="Contents"]]
180 -
181 181  == Offline ==
182 182  
183 -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>>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.
184 184  
185 185  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.
186 186  
187 -[[Contents>>doc:||anchor="Contents"]]
188 -
189 189  \\
190 190  
191 191  ----
192 192  
193 -**//
194 -//**
195 -
196 -\\
197 -
198 -\\
199 -
200 -\\
180 +**//NOTE~://** Content below the STOPPUBLISH variable is not published. Use this space as a scrap area.