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Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2026-01-19 14:35
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edited by sndueste
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1 1  == Contents ==
2 2  
3 3  
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5 5  {{toc/}}
6 6  
7 7  
8 -== General information about HDF5 and how to look on it ==
11 +== General information about HDF5 ==
9 9  
10 10  HDF5 is a data format maintained by the HDF group. For detailed general information see [[here>>url:https://portal.hdfgroup.org/display/support||shape="rect"]]
11 11  
12 -The easiest way to look at the HDF5 files from your beamtime is to use the Jupyter notebook interface to Maxwell:  [[https:~~/~~/max-jhub.desy.de/>>https://max-jhub.desy.de/]]
13 -
14 - The file content can be browsed by double clicking on the file.
15 -
16 -Typically the Jupyter notebook starts at your home directory and you have to create a (soft) link to your beamtime folder: open a terminal window (File->New-> Terminal) and create the link via :
17 -
18 -{{code language="none"}}> ln -sn beamtime path linkname
19 -e.g.
20 -> ln -sn /asap3/flash/gpfs/fl23/2025/data/11024321/ ~/beamtime_11024321 {{/code}}
21 -Then a “beamtime_11024321” folder should appear in your home directory.
22 -
23 -
24 -
25 -Alternativaly you can also use a conventional HDF viewer:
26 -
27 27  To download the HDF5 Viewer click [[here>>url:https://portal.hdfgroup.org/display/support/Download+HDFView||shape="rect"]]
28 28  
29 29  For use on the DESY Maxwell or PAL (max-fsc or pal) **hdfview** is available in the xray module :
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73 73  {{/expand}}
74 74  
75 75  === HDF examples: ===
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65 +{{/layout-section}}
76 76  
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77 77  * ADC data as example for **fast** **data** (10 Hz):            
78 78  
79 79  [[image:attach:image2020-11-16_15-26-28.png||height="250"]]
72 +{{/layout-cell}}
80 80  
74 +{{layout-cell}}
81 81  * The //average// FEL pulse energy as example for the **slow** **data**. Here the data is not saved with 10 Hz  - thus not for every FEL pulse train.  The data is typically saved with 1 Hz if the values are changing (like the FEL energy) and every about 20 sec if there is no change for longer time ( e.g. motor set values). Thus to use the data together with the "fast" one, one has to interpolate the data as explained in the examples in the repos below show (e.g. {{code language="none"}}df['GMD_T_average'] = df['GMD_T_average'].interpolate(method='linear'){{/code}})
82 82  
83 83   ( as example only every 10th train ID is listed in the HDF group "index")
84 84  
85 85  [[image:attach:image2020-11-16_15-31-45.png||height="250"]]
80 +{{/layout-cell}}
86 86  
82 +{{layout-cell}}
87 87  * (((
88 88  //zraw// group contains the **original DAQ (DOOCS) names**
89 89  )))
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92 92  
93 93  
94 94  [[image:attach:image2020-11-16_16-26-3.png||height="400"]]
91 +{{/layout-cell}}
92 +{{/layout-section}}
95 95  
94 +{{layout-section ac:type="single"}}
95 +{{layout-cell}}
96 96  {{info}}
97 97  === There are different options that help you to work with the FLASH HDF5 data in Python ===
98 98  
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99 99  * The currently developed option for large data sets: [[the FAB package>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]] ... see below
100 100  * and for smaller projects:  (% class="Object" %)[[https:~~/~~/gitlab.desy.de/christopher.passow/flash-daq-hdf>>url:https://gitlab.desy.de/christopher.passow/flash-daq-hdf||shape="rect"]]
101 101  
102 -(% class="Object" %)See also the collection of Demo data and sample scripts : [[Collection of HDF5 sample data from different beamlines>>doc:FLASHUSER.Offline data analysis (DAQ).Collection of HDF5 sample data from different beamlines.WebHome]] and [[DEMO - Working with FLASH data>>doc:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.WebHome]]
102 +(% class="Object" %)See also the collection of Demo data and sample scripts : [[doc:FS-FLASH USER tmp.Data Acquisition and controls 1.DAQ and controls overview.Offline data analysis (DAQ).Collection of HDF5 sample data from different beamlines.WebHome]] and [[doc:FS-FLASH USER tmp.Data Acquisition and controls 1.DAQ and controls overview.Offline data analysis (DAQ).DEMO - Working with FLASH data.WebHome]]
103 103  {{/info}}
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106 +{{/layout}}
104 104  
105 105  
106 106  
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108 108  
109 109  The complete list for the relation between DOOCS names and HDF5 names for the recordable parameters can be found in [[DESY's Repository>>url:https://stash.desy.de/projects/CS/repos/pah/browse/src/camp/data/channel2HdfName.dat||shape="rect"]].
110 110  
111 -== Most popular FLASH parameters and their names in HDF5, DOOCS and (.raw) DAQ ==
114 +== Most popular FLASH parameters and their names in HDF5, DOOCS and (raw) DAQ ==
112 112  
113 113  {{id name="DOOCSparameters"/}}
114 114  
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120 120  
121 121  The previously used naming scheme (2024 and before) can be found here:
122 122  
123 -{{expand expanded="false" title="FLASH1 naming scheme used until 2024"}}
126 +{{expand expanded="false" title="FLASH1 Naming scheme used until 2024"}}
124 124  ==== (% id="cke_bm_8853497S" style="display:none" %) (%%)Beamline info (FLASH1) ====
125 125  
126 126  {{code language="none"}}/FL1/Beamlines/Attenuator/pressure{{/code}}
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874 874  desc : The bunch number of the bunch used for the wavelength calculation
875 875  units :
876 876  
877 -{{expand expanded="false" title="More detailed info on OPIS properties"}}
878 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL370,'%','relative width of photoline in percent of the FEL photon energy ROI1, rising flank'
879 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL375,'%','relative width of photoline in percent of the FEL photon energy ROI1, tailing flank'
880 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL470,'%','relative width of photoline in percent of the FEL photon energy ROI1, mean'
881 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL371,'%','relative width of photoline in percent of the FEL photon energy ROI2, rising flank'
882 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL376,'%','relative width of photoline in percent of the FEL photon energy ROI2, tailing flank'
883 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL471,'%','relative width of photoline in percent of the FEL photon energy ROI2, mean'
884 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL372,'%','relative width of photoline in percent of the FEL photon energy ROI3, rising flank'
885 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL377,'%','relative width of photoline in percent of the FEL photon energy ROI3, tailing flank'
886 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL472,'%','relative width of photoline in percent of the FEL photon energy ROI3, mean'
887 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL373,'%','relative width of photoline in percent of the FEL photon energy ROI4, rising flank'
888 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL378,'%','relative width of photoline in percent of the FEL photon energy ROI4, tailing flank'
889 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL473,'%','relative width of photoline in percent of the FEL photon energy ROI4, mean'
890 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL374,'%','relative width of photoline in percent of the FEL photon energy ROI5, rising flank'
891 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL379,'%','relative width of photoline in percent of the FEL photon energy ROI5, tailing flank'
892 -FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL474,'%','relative width of photoline in percent of the FEL photon energy ROI5, mean'
893 -{{/expand}}
894 894  
895 895  If Opis is running typically on the the averaged data is saved. For several experiments it may make sense to save the information for each single bunch. This is up to now done by saving the complete ADC trace of the TOF setup. This is a huge amount of data and needs processing. This has to be performed after the beamtime in close contact to [[Markus Braune>>mailto:markus.braune@desy.de||shape="rect"]] ( responsible for [[OPIS>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/opis_spectrometer/index_eng.html||shape="rect"]])
896 896  
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935 935  desc: gap value of the undulators. This can be used to follow up how many undulators were closed and if there was a taper. 
936 936  units: mm
937 937  
938 -The gap values are saved for all 12 undulators (Nr 2 to 13). Undulator 13 is the one closest to the experimental hall.
924 +The gap values are saved for all 12 undulators (Nr 2 to 14). Undulator 14 is the one closest to the experimental hall.
939 939  
940 940  =====
941 941  arrival time (BAM) =====
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1219 1219  
1220 1220  {{view-file att--filename="FSLADAQ-DAQParameterlistFL24-2.pdf"}}{{/view-file}}
1221 1221  
1222 -internal link to parameter list: [[FS-LA DAQ - XWiki>>url:https://xwiki.desy.de/xwiki/bin/view/FSLADAQ/]]
1208 +
1223 1223  {{/info}}
1224 1224  
1225 1225  {{expand title="Laser parameters used until 2023"}}
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