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Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2026-01-19 14:35
From version 103.1
edited by sndueste
on 2025-11-12 14:55
Change comment: There is no comment for this version
To version 106.1
edited by sndueste
on 2026-01-09 15:29
Change comment: Uploaded new attachment "image.png", version {1}

Summary

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1 -{{layout}}
2 -{{layout-section ac:type="single"}}
3 -{{layout-cell}}
4 4  == Contents ==
5 5  
6 6  
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8 8  {{toc/}}
9 9  
10 10  
11 -== General information about HDF5 ==
8 +== General information about HDF5 and how to look on it ==
12 12  
13 13  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"]]
14 14  
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 +
15 15  To download the HDF5 Viewer click [[here>>url:https://portal.hdfgroup.org/display/support/Download+HDFView||shape="rect"]]
16 16  
17 17  For use on the DESY Maxwell or PAL (max-fsc or pal) **hdfview** is available in the xray module :
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61 61  {{/expand}}
62 62  
63 63  === HDF examples: ===
64 -{{/layout-cell}}
65 -{{/layout-section}}
66 66  
67 -{{layout-section ac:type="three_equal"}}
68 -{{layout-cell}}
69 69  * ADC data as example for **fast** **data** (10 Hz):            
70 70  
71 71  [[image:attach:image2020-11-16_15-26-28.png||height="250"]]
72 -{{/layout-cell}}
73 73  
74 -{{layout-cell}}
75 75  * 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}})
76 76  
77 77   ( as example only every 10th train ID is listed in the HDF group "index")
78 78  
79 79  [[image:attach:image2020-11-16_15-31-45.png||height="250"]]
80 -{{/layout-cell}}
81 81  
82 -{{layout-cell}}
83 83  * (((
84 84  //zraw// group contains the **original DAQ (DOOCS) names**
85 85  )))
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88 88  
89 89  
90 90  [[image:attach:image2020-11-16_16-26-3.png||height="400"]]
91 -{{/layout-cell}}
92 -{{/layout-section}}
93 93  
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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101 101  
102 102  (% 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]]
103 103  {{/info}}
104 -{{/layout-cell}}
105 -{{/layout-section}}
106 -{{/layout}}
107 107  
108 108  
109 109  
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877 877  desc : The bunch number of the bunch used for the wavelength calculation
878 878  units :
879 879  
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}}
880 880  
881 881  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"]])
882 882  
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