Changes for page DAQ and data analysis

Last modified by sndueste on 2025/02/05 14:56
From version 10.1
edited by sndueste
on 2019/08/06 13:14
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To version 12.1
edited by sendels
on 2019/08/08 09:00
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1 -XWiki.sndueste
1 +XWiki.sendels
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5 5  \\
6 6  
7 7  * Control and DAQ at FLASH (web version)
8 -** Overview
9 -** Things to consider before the beamtime
10 -** Beamline control and photon diagnostics
11 -** IT infrastructure
12 -** Data access
13 -** Online
14 -** Data acquisition
15 -** nearOnline
16 -*** .raw files
17 -*** HDF5 files
18 -** Offline
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"]]
19 19  
20 20  \\
21 21  
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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 +
34 34  == Things to consider before the beamtime ==
35 35  
36 36  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]].
37 37  
40 +[[Contents>>doc:||anchor="Contents"]]
41 +
38 38  == Beamline control and photon diagnostics ==
39 39  
40 40  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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50 50  [[jddd>>url:http://ttfinfo2.desy.de/doocs/jddd/index.html||title="jddd home" shape="rect"]]
51 51  )))
52 52  
57 +[[Contents>>doc:||anchor="Contents"]]
58 +
53 53  == IT infrastructure ==
54 54  
55 55  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"]].
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59 59  \\
60 60  
61 61  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]].
62 -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.
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.
63 63  
64 64  \\
65 65  
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83 83  )))|=(((
84 84  [[trigger via MTCA>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).Trigger Howto.WebHome]]
85 85  )))|=(((
86 -[[trainId via network>>doc:FLASHUSER.TrainID]]
92 +[[trainId via network>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).How to read Train IDs at FLASH.WebHome]]
87 87  )))
88 88  
89 -\\
95 +[[Contents>>doc:||anchor="Contents"]]
90 90  
91 91  == Data access ==
92 92  
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95 95  [[image:attach:timescale_dataAccess.png||height="400"]]
96 96  
97 97  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.
98 -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.
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: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.
99 99  
100 100  \\
101 101  
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121 121  after the beamtime
122 122  )))
123 123  
130 +[[Contents>>doc:||anchor="Contents"]]
131 +
124 124  == Online ==
125 125  
126 -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.
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.
127 127  
128 128  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.
129 129  
138 +[[Contents>>doc:||anchor="Contents"]]
139 +
130 130  == Data acquisition ==
131 131  
132 -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.
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.
133 133  
134 134  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.
135 135  
136 -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"]].
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"]].
137 137  
138 138  \\
139 139  
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141 141  |=(((
142 142  [[DAQ introductions>>attach:Operator_training_DAQ_May_2016.pdf]]
143 143  )))|=(((
144 -[[FLASH1 PBD>>doc:FLASHUSER.PBD DAQ]]
154 +[[FLASH1 PBD>>doc:FLASHUSER.FLASH1 PhotDiag stream]]
145 145  )))|=(((
146 -[[FLASH2 PBD>>doc:FLASHUSER.FL2PhotDiag stream (status Feb 2017)]]
156 +[[FLASH2 PBD>>doc:FLASHUSER.FLASH2 PhotDiag stream]]
147 147  )))|=(((
148 148  [[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]]
149 149  )))|=(((
150 -[[User DAQs subsytems>>doc:FLASHUSER.Description of the Properties in the FLASH1_USER1, 2 and 3 for FLASH1 Users]]
160 +[[User DAQs subsytems>>doc:FLASHUSER.Configuring the user DAQs]]
151 151  )))|=(((
152 -[[HDF5 files>>doc:FLASHUSER.Information about the FLASH HDF5 structure]]
162 +[[HDF5 files>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]]
153 153  )))
154 154  
165 +[[Contents>>doc:||anchor="Contents"]]
166 +
155 155  == nearOnline ==
156 156  
157 157  ==== .raw files ====
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162 162  
163 163  ==== HDF5 files ====
164 164  
165 -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.
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.
166 166  
179 +[[Contents>>doc:||anchor="Contents"]]
180 +
167 167  == Offline ==
168 168  
169 -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.
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.
170 170  
171 171  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.
172 172  
187 +[[Contents>>doc:||anchor="Contents"]]
188 +
173 173  \\
174 174  
175 175  ----