Wiki source code of DAQ and data analysis

Version 37.4 by sndueste on 2025/02/05 14:55
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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>>url:http://photon-science.desy.de/facilities/flash/beamlines/daq_and_controls/index_eng.html||shape="rect"]].
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3 == Contents ==
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7 {{toc/}}
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10 ----
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12 == Overview ==
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14 [[image:attach:overview_flash_control_and_daq.png]]
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16 The FLASH accelerator, beamlines and experiments are using the Distributed Object Oriented Control System ([[DOOCS>>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>>https://doocs.desy.de/||shape="rect"]]) by the FLASH team or the users themself. Further it is provided a DOOCS client API 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>>url:https://ttfinfo.desy.de/elog/showElogs.jsp||shape="rect"]]  (only inside the DESY network) available in which jddd and other software can print directly.
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18 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.
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20 [[Contents>>doc:||anchor="Contents"]]
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22 == Things to consider before the beamtime ==
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24 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]].
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26 [[Contents>>doc:||anchor="Contents"]]
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28 == Beamline control and photon diagnostics ==
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30 Use existing jddd panel provided by FLASH or use the jddd editor to create a new panel according to the user's own needs.
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33 [[ >>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:attach:image2023-2-13_13-4-52.png||height="250"]] [[~[~[image:attach:image2023-2-13_13-5-51.png~|~|height="250"~]~]>>url:https://jddd.desy.de/||shape="rect"]]
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36 (% class="wrapped" %)
37 |=(((
38 [[DOOCS>>url:https://doocs-web.desy.de/index.html||shape="rect"]]
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40 [[jddd>>url:https://jddd.desy.de/||shape="rect"]]
41 )))
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43 [[Contents>>doc:||anchor="Contents"]]
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45 == IT infrastructure ==
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47 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>>https://docs.desy.de/asap3/||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>>https://docs.desy.de/maxwell/||shape="rect"]]and [[JupyterHub on Maxwell>>url:https://confluence.desy.de/display/MXW/JupyterHub+on+Maxwell||shape="rect"]] (see also: (% class="plugin_pagetree_children_span" %)[[ComputingResourcesUserGuide>>url:https://confluence.desy.de/display/FLASHUSER/ComputingResourcesUserGuide?src=contextnavpagetreemode||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>>https://docs.desy.de/asap3/||shape="rect"]]
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49 [[image:attach:it-infrastructure2.png||height="400"]]
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52 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]].
53 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.
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58 [[local>>attach:jddd.jnlp]][[ machines>>attach:jddd.jnlp]]
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60 (% class="content-wrapper" %)
61 (((
62 [[Maxwell cluster>>https://docs.desy.de/maxwell/||shape="rect"]]
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65 [[doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).MTCA ADCs.WebHome]]
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67 [[supported devices>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).DOOCS Device Support.WebHome]]
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71 [[supported cameras>>url:https://ttfinfo.desy.de/FLASHWiki/Wiki.jsp?page=Camera%20server||shape="rect"]]
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73 )))|=(((
74 [[trigger via MTCA>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).Trigger Howto.WebHome]]
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76 [[trainId via network>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).How to read Train IDs at FLASH.WebHome]]
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79 [[Contents>>doc:||anchor="Contents"]]
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81 == Data access ==
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84 [[image:attach:timescale_dataAccess.png||height="400"]]
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86 At the Free-electron Laser Hamburg ([[FLASH>>url:https://flash.desy.de/||shape="rect"]]) we use the Distributed Object Oriented Control System ([[DOOCS>>http://doocs.desy.de/||shape="rect"]]). Devices are implemented via DOOCS servers and via an API it is possible to request data directly from the DOOCS server by knowing the DOOCS address.
87 As correlations of different physical properties are often required all data at FLASH are indexed by [[train IDs>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).How to read Train IDs at FLASH.WebHome]], which identify each of FLASH's pulse train. The during a beamtime recorded data are stored via a Data Acquisition System ([[DAQ>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).WebHome]]) which sort all events from the individual DOOCS server by train ID. When requested [[HDF files>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.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 as well as the data created by the 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 HDF "slices" via a {{code language="none"}}nearOnline{{/code}} converter within a few minutes. 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.DAQ and controls overview.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.
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92 online
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94 live at 10 Hz
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97 online via DAQmonitor
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99 live up to 3s into the past
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102 nearOnline
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104 a few minutes
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107 offline
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109 after the beamtime
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112 [[Contents>>doc:||anchor="Contents"]]
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114 == Online ==
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116 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 [[Python>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Online data analysis.PythonDOOCS.WebHome]].  For accessing the control system [[DOOCS addresses>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]] are required.
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119 [[Contents>>doc:||anchor="Contents"]]
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121 == Data acquisition ==
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123 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.DAQ and controls overview.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>>url:https://confluence.desy.de/display/ASAP3/Architecture||shape="rect"]] formerly known as ASAP3/GPFS, is access regulated via [[DOOR>>url:https://door.desy.de/door/index.php||shape="rect"]] and only registered participants have access.
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125 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.
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127 While the DOOCS addresses are rather cryptic the [[HDF5 file>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.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 software repository>>url:https://stash.desy.de/projects/FSFL/repos/pydaq-test/raw/src/pydaqh5/dat/channel2HdfName.dat?at=refs%2Fheads%2Fmaster||shape="rect"]].
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132 [[DAQ introductions>>attach:Operator_training_DAQ_May_2016.pdf]]
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134 [[User DAQs>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).How to save data in the User DAQ.WebHome]]
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136 [[HDF5 files>>doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]]
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139 [[Contents>>doc:||anchor="Contents"]]
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141 == Offline ==
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143 The nearOnline HDF slices are available offline too on the spectrum scale file system. Access is granted from the within the DESY network for beamtime participants (see (% class="plugin_pagetree_children_span" %)[[ComputingResourcesUserGuide>>url:https://confluence.desy.de/display/FLASHUSER/ComputingResourcesUserGuide?src=contextnavpagetreemode||shape="rect"]](%%)) or from the outside via [[Gamma portal>>url:https://confluence.desy.de/display/ASAP3/The+Gamma+Portal||shape="rect"]]. HDF files can processed with common tools, e.g. with Python, 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.
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145 The spectrum scale file system contains the [[substructure>>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.
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