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Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2026-01-19 14:35
From version 106.1
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: ===
64 +{{/layout-cell}}
65 +{{/layout-section}}
76 76  
67 +{{layout-section ac:type="three_equal"}}
68 +{{layout-cell}}
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}}
104 +{{/layout-cell}}
105 +{{/layout-section}}
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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788 788  
789 789  
790 790  {{code language="none"}}/FL2/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
794 +//always saved (PBD2)//
791 791  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL/INTENSITY.TD{{/code}}
792 792  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL/INTENSITY.TD{{/code}}
793 793  desc : Energy per pulse measured in the Tunnel  (in front of the gas attenuator and the apertures in the Hall) In addition measurement errors and beam position are included for EACH pulse in the pulse train  !! (see below)
... ... @@ -822,6 +822,7 @@
822 822  
823 823  
824 824  {{code language="none"}}/FL2/Photon Diagnostic/GMD/Average Beam position/position tunnel horizontal{{/code}}
829 +//always saved (PBD2)//
825 825  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IX.POS{{/code}}
826 826  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IX.POS{{/code}}
827 827  desc : the Average ( ~~ 20 sec averaging time ) Beam position of the photon Beam determined by the GMD (tunnel, x=horizontal)
... ... @@ -829,6 +829,7 @@
829 829  
830 830  
831 831  {{code language="none"}}/FL2/Photon Diagnostic/GMD/Average Beam position/position tunnel vertical{{/code}}
837 +//always saved (PBD2)//
832 832  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IY.POS{{/code}}
833 833  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IY.POS{{/code}}
834 834  desc : the Average ( ~~ 20 sec averaging time ) Beam position of the photon Beam determined by the GMD (tunnel, x=horizontal)
... ... @@ -836,6 +836,7 @@
836 836  
837 837  
838 838  /FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position tunnel x
845 +always saved (PBD2)
839 839  DOOCS prop : FLASH.FEL/XGM.BPM/FL2.HALL/X.TD
840 840  DAQ channel: FLASH.FEL/XGM.BPM/FL2.HALL:2
841 841  desc: Besides the well calibrated averaged beam position information there is also the option to measure the beam position on a single bunch level. HOWEVER this methide needs a perfectly adjusted signal level (talk to your local contact !!) and also then the signal to noise is rather small and one needs some averaging ... BUT with this option one can determine if there was a spatial slope on a burst (say forst bunches were lower than the last ones or so ...)
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855 855  
856 856  
857 857  {{code language="none"}}/FL2/Photon Diagnostic/Wavelength/OPIS tunnel/Processed/mean photon energy{{/code}}
865 +// saved opon request (PBD2)//
858 858  DOOCS prop : {{code language="none"}}FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL042{{/code}}
859 859  DAQ channel:{{code language="none"}} FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL042{{/code}}
860 860  desc : mean photon energy ( ~~ 1 sec averaging time ) measured in the TUNNEL for a specific bunch out of the bunch train (via photoelectron spectroscopy)
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862 862  
863 863  
864 864  {{code language="none"}}/FL2/Photon Diagnostic/Wavelength/OPIS tunnel/Processed/mean wavelength{{/code}}
873 +// saved opon request (PBD2)//
865 865  DOOCS prop : {{code language="none"}}FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL040{{/code}}
866 866  DAQ channel:{{code language="none"}} FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL040{{/code}}
867 867  desc : mean wavelength ( ~~ 1 sec averaging time ) measured in the TUNNEL for a specific bunch out of the bunch train (via photoelectron spectroscopy)
... ... @@ -869,28 +869,12 @@
869 869  
870 870  
871 871  {{code language="none"}}/FL2/Photon Diagnostic/Wavelength/OPIS tunnel/Processed/number of analyzed bunch        (in older version this can be found in OPIS tunnel/Expert stuff/General operation parameters/){{/code}}
881 +// saved opon request (PBD2)//
872 872  DOOCS prop : {{code language="none"}}FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL060{{/code}}
873 873  DAQ channel:{{code language="none"}} FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL060{{/code}}
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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904 904  ===== bunch charge =====
905 905  
906 906  {{code language="none"}}/FL2/Electron Diagnostic/Bunch charge/after undulator{{/code}}
900 +//always saved (PBD2)//
907 907  DOOCS prop : {{code language="none"}}FLASH.DIAG/PBD2.TOROID.ML/9FL2BURN/CHARGE.FLASH2{{/code}}
908 908  DAQ channel: {{code language="none"}}FLASH.DIAG/PBD2.TOROID.ML/9FL2BURN/CHARGE.FLASH2{{/code}}
909 909  desc: electron bunch charge FLASH2 (average value for each bunchtrain).
... ... @@ -913,6 +913,7 @@
913 913  ===== electron bunch energy =====
914 914  
915 915  {{code language="none"}}/FL2/Electron Diagnostic/Electron energy/energy of first bunch/behind undulators{{/code}}
910 +//always saved (PBD2)//
916 916  DOOCS prop : {{code language="none"}}FLASH.DIAG/BEAM_ENERGY_MEASUREMENT/FL2XTDS/ENERGY.FLASH2{{/code}}
917 917  DAQ channel: (% style="color:#5e6c84" %)TTF2.DAQ/PBD2.BEAM.ENERGY.MEAS.ML.COPY/FL2XTDS.ENERGY.FLASH2{{code language="none"}}{{/code}}(%%)
918 918  desc: electron bunch energy measured behind the undulator. Data is saved with 10 Hz - BUT (for computation reasons) only the energy of the FIRST bunch is recorded. The data is also available for (% style="color:#5e6c84" %)extraction and septum  in the beginning of FLASH2
... ... @@ -923,19 +923,21 @@
923 923  (% style="color: rgb(94, 108, 132); font-weight: 600; letter-spacing: 0px;" %)
924 924  ===== undulator settings =====
925 925  
926 -{{code language="none"}}/FL2/Electron Diagnostic/Undulator setting/set wavelength 1{{/code}}
927 -DOOCS prop : {{code language="none"}}FLASH.FEL/FL2.WAVELENGTHCONTROL/FLASH2.COLOR1/WAVELENGTH{{/code}}
928 -DAQ channel:  {{code language="none"}}FLASH.FEL/FL2.WAVELENGTHCONTROL/FLASH2.COLOR1/WAVELENGTH{{/code}}
929 -desc: Set value for the anticipated wavelength 1 . This parameter is used to set the undulator gap. It may however deviate from the actual wavelength by several % ... For 2 color operation there is also  the same parameter for COLOR 2
921 +{{code language="none"}}/FL2/Electron Diagnostic/Undulator setting/set wavelength{{/code}}
922 +//always saved (PBD2)//
923 +DOOCS prop : {{code language="none"}}TTF2.FEEDBACK/FL2.WAVELENGTHCONTROL/FLASH2/WAVELENGTH{{/code}}
924 +DAQ channel:  {{code language="none"}}TTF2.FEEDBACK/FL2.WAVELENGTHCONTROL/FLASH2/WAVELENGTH{{/code}}
925 +desc: Set value for the anticipated wavelength . This parameter is used to set the undulator gap. It may however deviate from the actual wavelength by several % ...
930 930  units: nm
931 931  
932 -{{code language="none"}}/FL2/Electron Diagnostic/Undulator setting/SASE13 gap{{/code}}
933 -DOOCS prop : {{code language="none"}}FLASH.UTIL/FL2.UND.MOTOR/FL2SASE13/GAP{{/code}}
934 -DAQ channel:  {{code language="none"}}FLASH.UTIL/FL2.UND.MOTOR/FL2SASE13/GAP{{/code}}
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. 
928 +{{code language="none"}}/FL2/Electron Diagnostic/Undulator setting/SASE14 gap{{/code}}
929 +//always saved (PBD2)//
930 +DOOCS prop : {{code language="none"}}FLASH.UTIL/FL2.UND.MOTOR/FL2SASE14/GAP{{/code}}
931 +DAQ channel:  {{code language="none"}}FLASH.UTIL/FL2.UND.MOTOR/FL2SASE14/GAP{{/code}}
932 +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.
935 +The gap values are saved for all 12 undulators (Nr 3 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/]]
1219 +
1223 1223  {{/info}}
1224 1224  
1225 1225  {{expand title="Laser parameters used until 2023"}}
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