Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2025/02/06 10:55
From version 41.1
edited by sndueste
on 2021/02/09 14:40
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To version 38.1
edited by sndueste
on 2021/02/09 10:51
Change comment: There is no comment for this version

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... ... @@ -18,61 +18,8 @@
18 18  
19 19  [[Contents>>doc:||anchor="Contents"]]
20 20  
21 -== The new (starting 2021) HDF5 format ==
21 +== The current FLASH HDF5 structure ==
22 22  
23 -\\
24 -
25 -FLASH provides a conversion of its data acquisition (DAQ) to the commonly used [[HDF5>>url:https://www.hdfgroup.org/solutions/hdf5/||shape="rect"]] format. Correlated  data are mapped by a primary index called **train ID**. Every data set has an individual index of train IDs to identify the data even when data are missing or deviate in update rate.If the data set of choice contains gaps,  users have to decide how to treat missing values. DAQ channels are spread across various files with one file name pattern for each DAQ. This means users have to assemble data from different files if necessary.
26 -
27 -The hierarchy is realized using a human readable named HDF tree with each DAQ channel containing the data sets "//value//" and "//index//". Additionally, the HDF group //zraw// contains a tree of the original DAQ channel names.
28 -
29 -Reference implementation, which follows the concept of Python libraries like Pandas, Xarray, or Dask, is given below.
30 -
31 -\\
32 -
33 -{{expand title="Discontinued HDF formats"}}
34 -== Comparison to FLASH's deprecated HDF formats ==
35 -
36 -Before 2021, FLASH provided two different HDF formats formally known as //near-online// and //offline// HDF files.
37 -
38 -All data sets were aligned by the same global index by filling in missing data. Fast DAQ channels  (pulse synchronous data - update 10 Hz) are filled in by NaN or 0, slow channels (not pulse synchronous data - update e.g. 1 Hz ) are interpolated by the DAQs libraries, by keeping the value constant up to the next change.
39 -
40 -While the near-online HDF files were converted live during the beamtime, the offline HDF files were manually compiled weeks/months later. Near-online HDF files were used by a provided API [[BeamtimeDaqAccess>>url:https://confluence.desy.de/display/FLASHUSER/Near-Online+data+analysis#Near-Onlinedataanalysis-BriefUserGuidetoBeamtimeDAQAccess||shape="rect"]], which also searches for DAQ channels in files. With assembled files "by run", all DAQ channels were existing in the same HDF file. While shorter runs usually fitted into one file, longer runs still had to be aggregated over several files. The creation of the assembled type of files still involves the use of fairly unstable DAQ Mex-functions As the environment required for using the Mex-functions is already deprecated, its continued existence is uncertain.
41 -
42 -The HDF hierarchy is almost identical in all formats. While in the the recent format each DAQ channel contains the data sets "value" and "index", the deprecated format had one data set for each DAQ channel. The deprecated formats supplies no time axis parameters for spectra data types.
43 -{{/expand}}
44 -
45 -== HDF excerpt: ==
46 -
47 -* ADC data as example for **fast** **data** (10 Hz):            [[image:attach:image2020-11-16_15-26-28.png||height="250"]]
48 -* The //average// FEL pulse energy as example for the **slow** **data** (different e.g. 1 Hz):[[image:attach:image2020-11-16_15-31-45.png||height="250"]]
49 -
50 - ( every 10th train ID is listed in the HDF group "index")
51 -
52 -* (((
53 -//zraw// group contains the **original DAQ (DOOCS) names[[image:attach:image2020-11-16_16-26-3.png||thumbnail="true" height="250"]]**
54 -)))
55 -
56 - of the properties saved in the DESY internal raw format. (For experts)
57 -
58 -\\
59 -
60 -\\
61 -
62 -{{info title="Sample scripts in python"}}
63 -== Reference implementation (Python) ==
64 -
65 -[[~[~[image:attach:binder_badge.png~|~|thumbnail="true" width="120"~]~]>>url:https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.desy.de%2Fchristopher.passow%2Fflash-daq-hdf/master||shape="rect"]]
66 -
67 -(% class="Object" %)[[https:~~/~~/gitlab.desy.de/christopher.passow/flash-daq-hdf>>url:https://gitlab.desy.de/christopher.passow/flash-daq-hdf||shape="rect"]]
68 -{{/info}}
69 -
70 -\\
71 -
72 -\\
73 -
74 -== The discontinued (till 2021) FLASH HDF5 structure ==
75 -
76 76  The photon diagnostic, electron diagnostic and beamline information as well as the information about the pump-probe laser and the infrastructure offered for users (GHz/MHz ADCs) can be included in one HDF5 file which is organized according to train IDs. The general structure is:
77 77  
78 78  * Electron Diagnostic
... ... @@ -89,7 +89,7 @@
89 89  
90 90  \\
91 91  
92 -=== HDF5 example files (old format) ===
39 +=== HDF5 example files ===
93 93  
94 94  Here we have a few HDF5 samples (User data combined with Photon diagnostics data) from a few beamtimes showing the different kind options.
95 95  
... ... @@ -107,6 +107,14 @@
107 107  
108 108  \\
109 109  
57 +== The new (starting 2021) HDF5 format ==
58 +
59 +Here is [[some documentation on the changes of the HDF5 format>>doc:FLASHUSER.HDF5 format]] that well be available in 2021 (work in progress)
60 +
61 +\\
62 +
63 +\\
64 +
110 110  == Most popular FLASH parameters and their names in HDF5, DOOCS and (raw) DAQ ==
111 111  
112 112  {{id name="DOOCSparameters"/}}
... ... @@ -196,14 +196,12 @@
196 196  
197 197  \\
198 198  
199 -==== Photon Diagnostics SASE ([[GMD>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/gmd_intensity_and_position/index_eng.html||shape="rect"]]) ====
154 +==== Photon Diagnostics SASE ([[GMD>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/gmd_intensity_and_position/index_eng.html||shape="rect"]]) / Spectrometer (FLASH1) ====
200 200  
201 -\\
202 -
203 -(% style="color: rgb(0,0,0);" %)**Discontinued GMD data recording / evaluation  (VME + PhotonFlux ML server)**
204 -
205 205  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
206 -//always saved (PBD)//
157 +//always saved (PBD)//
158 +(% style="color: rgb(165,173,186);" %)New MTCA Version: DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}} (%%)
159 +(% style="color: rgb(165,173,186);" %)New MTCA Version: DAQ channel: {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}}
207 207  
208 208  (% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT04/VAL{{/code}} (%%)
209 209  (% style="color: rgb(0,0,0);" %)DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENPULSEIC{{/code}}(%%)
... ... @@ -213,6 +213,9 @@
213 213  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
214 214  //always saved (PBD)//
215 215  
169 +(% style="color: rgb(193,199,208);" %)New MTCA Version: DOOCS prop : 
170 +{{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL1.TUNNEL/INTENSITY.TD{{/code}}New MTCA Version: DAQ channel: {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL1.TUNNEL/INTENSITY.TD{{/code}}
171 +
216 216  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT34/VAL{{/code}}
217 217  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.USER{{/code}}
218 218  desc :Energy per pulse Tunnel (from e-) - the values are set to "0" if there was no SASE beam in the FEL
... ... @@ -228,6 +228,9 @@
228 228  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy BDA{{/code}}
229 229  //always saved (PBD)//
230 230  
187 +(% style="color: rgb(165,173,186);" %)New MTCA Version: DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.BDA/PHOTONFLUX.UJ{{/code}} (%%)
188 +(% style="color: rgb(165,173,186);" %)New MTCA Version: DAQ channel: {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.BDA/PHOTONFLUX.UJ{{/code}}
189 +
231 231  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT05/VAL{{/code}}
232 232  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENPULSEIC{{/code}}
233 233  desc : calibrated average SASE Energy/pulse measured in the BDA (in the experimental hall) after the attenuator (ion current)
... ... @@ -236,6 +236,8 @@
236 236  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA{{/code}}
237 237  //always saved (PBD)//
238 238  
198 +(% style="color: rgb(193,199,208);" %)New MTCA Version: DOOCS prop : 
199 +{{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL1.BDA/INTENSITY.TD{{/code}}New MTCA Version: DAQ channel: {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL1.BDA/INTENSITY.TD{{/code}}(%%)
239 239  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT35/VAL{{/code}}
240 240  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.USER{{/code}}
241 241  desc :Energy per pulse BDA (from e-) - the values are set to "0" if there was no SASE beam in the FEL
... ... @@ -250,55 +250,6 @@
250 250  
251 251  \\
252 252  
253 -(% style="color: rgb(0,0,0);" %)**NEW (2021) GMD data recording / evaluation  (MTCA, analog to FLASH2 and XFEL)**
254 -
255 -{{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
256 -//always saved (PBD)//
257 -(% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}} (%%)
258 -(% style="color: rgb(0,0,0);" %)DAQ channel: {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}}
259 -
260 -desc : calibrated average SASE Energy/pulse measured in the TUNNEL upstream the gas attenuator
261 -units : microJ
262 -
263 -\\
264 -
265 -{{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
266 -//always saved (PBD)//
267 -
268 -(% style="color: rgb(0,0,0);" %)DOOCS prop : 
269 -{{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL1.TUNNEL/INTENSITY.TD{{/code}}DAQ channel: {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL1.TUNNEL/INTENSITY.TD{{/code}}
270 -
271 -desc : Energy per pulse measured in the Tunnel.  In addition measurement errors and beam position are included for EACH pulse in the pulse train  !! (see below)
272 -units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision)** [[see here for help>>doc:FLASHUSER.jddd-linked help pages.Calibrating the pulse resolved (electron) data from GMD.WebHome]]**
273 -
274 -{{info title="GMD pulse resolved data structure"}}
275 -For every pulse in the pulse train the information is saved:
276 -
277 -
278 -1. **Intensity per pulse** (a.u. (more or less µJ ))
279 -1. Intensity per pulse (auxillary GMD) - not used
280 -1. Position horizontal (mm, for a single pulse the position information may be very noisy  - talk to your local contact)
281 -1. Position vertical (mm, for a single pulse the position information may be very noisy  - talk to your local contact)
282 -1. **Intensity per pulse sigma** (a.u. (more or less µJ ), (% style="color: rgb(0,0,0);" %)This parameter gives an indication of the error of the measurement of the pulse energy. This takes signal to noise,  detector resolution, uncertainties in crossection etc into account. (it is NOT the measurement of the statistical fluctuation of the SASE pulses)(%%))
283 -1. Position horizontal sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
284 -1. Position vertical sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
285 -1. Combined warning and error flags
286 -
287 -The pulse energy and the error are plotted for the first bunch of the pulse trains saved in this 
288 -file
289 -
290 -
291 -[[image:attach:image2021-2-9_10-51-6.png||height="250"]]
292 -
293 -\\
294 -{{/info}}
295 -
296 -All values for the GMD are also available for the** BDA GMD **which is located in the experimental hall down stream the gas attenuator. If the attenuator is on the ratio between BDA and Tunnel signal shows the attenuation. **BUT NOTE** that the filter units  are downstream the GMD. So if filters  are used this influence is NOT measured by the GMD BDA !
297 -
298 -\\
299 -
300 -Besides  pulse energy the GMD also provides information about the beam position
301 -
302 302  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA horizontal{{/code}}
303 303  //always saved (PBD)//
304 304  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
... ... @@ -327,10 +327,6 @@
327 327  desc :Beam position of the photon Beam determined by the GMD (TUNNEL, y=vertical)
328 328  units : mm
329 329  
330 -\\
331 -
332 -==== Spectrometer (FLASH1) ====
333 -
334 334  {{code language="none"}}/FL1/Photon Diagnostic/Wavelength/Tunnelspectrometer/wavelength{{/code}}
335 335  _always saved (when Spectrum is measured !!) (PBD) _
336 336  DOOCS prop : {{code language="none"}}TTF2.EXP/PHOTONWL.ML/WAVE_LENGTH/VAL.TD{{/code}}
... ... @@ -461,7 +461,7 @@
461 461  ===== electron bunch energy =====
462 462  
463 463  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/average electron energy{{/code}}
464 -//always saved (PBD)//
372 +_always saved (PBD)
465 465  DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/E_INTRA_MEAN/VAL{{/code}}
466 466  DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/E_MEAN{{/code}}
467 467  desc: electron bunch energy (average over the bunch train)
... ... @@ -469,7 +469,7 @@
469 469  \\
470 470  
471 471  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/pulse resolved energy{{/code}}
472 -//always saved (PBD)//
380 +_always saved (PBD)
473 473  DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/E_SPECT/VAL.TD{{/code}}
474 474  DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/E_SPECT{{/code}}
475 475  desc: electron bunch energy bunch resolved
... ... @@ -478,7 +478,7 @@
478 478  \\
479 479  
480 480  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/wavelength bunch train average{{/code}}
481 -//always saved (PBD)//
389 +_always saved (PBD)
482 482  DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/LAMBDA_MEAN/VAL{{/code}}
483 483  DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/LAMBDA_MEAN{{/code}}
484 484  desc: Wavelength calculated by the electron bunch energy (average over the bunch train) (FLASH1)
... ... @@ -672,12 +672,12 @@
672 672  
673 673  ==== Beamline info (FLASH2) ====
674 674  
675 -{{code language="none"}}/FL2/Beamlines/Attenuator/pressure  {{/code}}
676 -(% style="color: rgb(0,0,0);" %)//always saved (PBD2)// (%%)
677 -(% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
678 -(% style="color: rgb(0,0,0);" %)DAQ channel:  {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
679 -(% style="color: rgb(0,0,0);" %)desc: set pressure in the gas attenuator (%%)
680 -(% style="color: rgb(0,0,0);" %)units: mbar(%%)
583 +(% style="color: rgb(255,153,0);" %)(not yet available){{code language="none"}}/FL2/Beamlines/Attenuator/pressure  {{/code}}(%%)
584 +(% style="color: rgb(193,199,208);" %)//always saved (PBD2)// (%%)
585 +(% style="color: rgb(193,199,208);" %)DOOCS prop : {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
586 +(% style="color: rgb(193,199,208);" %)DAQ channel:  {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
587 +(% style="color: rgb(193,199,208);" %)desc: set pressure in the gas attenuator (%%)
588 +(% style="color: rgb(193,199,208);" %)units: mbar(%%)
681 681  \\
682 682  
683 683  {{code language="none"}}/FL2/Beamlines/FL20/Shutter/open{{/code}}
... ... @@ -696,13 +696,11 @@
696 696  units: degree
697 697  \\
698 698  
699 -/FL2/Beamlines/Filter wheel/position wheel 2
700 -always saved (PBD2)
701 -DOOCS prop : {{code language="none"}}FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS{{/code}}
702 -DAQ channel: {{code language="none"}}FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS{{/code}}
703 -desc: Position of the BL filter wheel 2 - to correlate with the filter material please look [[here>>doc:FLASHUSER.jddd-linked help pages.Filter-Units.Filter wheels in FLASH1 and FLASH2.WebHome]]
704 -units: degree
705 705  
608 +//always saved (PBD2)//
609 +\\\\**[[here>>doc:FLASHUSER.jddd-linked help pages.Filter-Units.Filter wheels in FLASH1 and FLASH2.WebHome]]**
610 +{{code language="none"}}/FL2/Beamlines/Filter wheel/position wheel 2 DOOCS prop : FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS DAQ channel: FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS desc: Position of the BL filter wheel 2 - to correlate with the filter material please look units: degree{{/code}}
611 +
706 706  \\
707 707  
708 708  NOTE: Aperture positions in the beamline as well as the positions of the beam steering mirrors are also saved. for more Info contact your local contact
... ... @@ -731,14 +731,13 @@
731 731  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)
732 732  units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision)** [[see here for help>>doc:FLASHUSER.jddd-linked help pages.Calibrating the pulse resolved (electron) data from GMD.WebHome]]**
733 733  
734 -{{info title="GMD pulse resolved data structure"}}
735 735  For every pulse in the pulse train the information is saved:
736 736  
737 737  
738 738  1. **Intensity per pulse** (a.u. (more or less µJ ))
739 739  1. Intensity per pulse (auxillary GMD) - not used
740 -1. Position horizontal (mm, for a single pulse the position information may be very noisy  - talk to your local contact)
741 -1. Position vertical (mm, for a single pulse the position information may be very noisy  - talk to your local contact)
645 +1. Position horizontal (mm, for a single pulse the position informytion may be very noisy  - talk to your local contact)
646 +1. Position vertical (mm, for a single pulse the position informytion may be very noisy  - talk to your local contact)
742 742  1. **Intensity per pulse sigma** (a.u. (more or less µJ ), (% style="color: rgb(0,0,0);" %)This parameter gives an indication of the error of the measurement of the pulse energy. This takes signal to noise,  detector resolution, uncertainties in crossection etc into account. (it is NOT the measurement of the statistical fluctuation of the SASE pulses)(%%))
743 743  1. Position horizontal sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
744 744  1. Position vertical sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
... ... @@ -750,10 +750,8 @@
750 750  
751 751  [[image:attach:image2021-2-9_10-51-6.png||height="250"]]
752 752  
753 -\\
754 -{{/info}}
755 755  
756 -\\
659 +{{code language="none"}}{{/code}}
757 757  
758 758  All values for the GMD are also available for the** HALL GMD **which is located in the experimental hall down stream the gas attenuator. If the attenuator is on the ratio between Hall and Tunnel signal shows the attenuation. **BUT NOTE** that the filter unit and the Aperture 4 are downstream the GMD. So if filters and aperture are used this influence is NOT measured by the GMD hall !
759 759  
... ... @@ -781,15 +781,13 @@
781 781  
782 782  \\
783 783  
784 -/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position tunnel x
785 -always saved (PBD2)
786 -DOOCS prop : FLASH.FEL/XGM.BPM/FL2.HALL/X.TD
787 -DAQ channel: FLASH.FEL/XGM.BPM/FL2.HALL:2
788 -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 ...)
789 -units : mm   
790 790  
791 -(x=horizontal, y = vertial)
688 +//always saved (PBD2)//
689 +\\\\{{code language="none"}}/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position tunnel x DOOCS prop : FLASH.FEL/XGM.BPM/FL2.HALL/X.TDDAQ channel: FLASH.FEL/XGM.BPM/FL2.HALL:2 desc: {{/code}}Besides the well calibrated averaged beam position information there is also the option
690 +{{code language="none"}}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 ...)units : mm    {{/code}}
792 792  
692 +{{code language="none"}}(x=horizontal, y = vertial){{/code}}
693 +
793 793  again the same parameter set is available for the **HALL GMD**
794 794  
795 795  \\
... ... @@ -1190,14 +1190,63 @@
1190 1190  
1191 1191  \\
1192 1192  
1193 -== HDF5 and DOOCS ==
1094 +=== Samples how to read HDF5 with Matlab ===
1194 1194  
1195 -Here is an outdated [[list with the available properties that are always saved (PBD) for FLASH1 as>>attach:FLASH1__DaqChannel2HdfNamePbd.xlsx]] HDF5 names and the corresponding DOOCS names
1096 +The examples apply to HDF files with HDF tree version before vers. 0.3.0.
1196 1196  
1197 -[[Contents>>doc:||anchor="Contents"]]
1098 +(% style="color: rgb(0,128,0);" %)%% read in the needed data p=path; path(p,'D:\mess-daten\DAQ-data\hdf5\Gotthard') % add the actual folder to the path hdf5file='FLASH1_EXP-2016-03-16T1420.h5'; % data with Gotthard and VLS
1198 1198  
1199 -\\
1100 +(% style="color: rgb(0,128,0);" %)% h5disp(hdf5file,'/','min') % to get an idea what is in the file % h5info(hdf5file,'/Experiment/Gotthard1/BL.0') % get info about the individual channel
1200 1200  
1102 +(% style="color: rgb(0,128,0);" %)% read a Number per 10 Hz pulse train:
1103 +
1104 +(% class="code" %)
1105 +(((
1106 +FEL_Wavelength_energy_server=h5read(hdf5file,'/Photon Diagnostic/Wavelength/Calculated by energy/wavelength' );
1107 +)))
1108 +
1109 +(% style="color: rgb(0,128,0);" %)% read in a 1D array (spectrum) %GMD data GMD_Spectrum=h5read(hdf5file,'/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA');
1110 +
1111 +(% style="color: rgb(0,128,0);" %)% This reads in all the data . One can also limit the amount of data read to a subset of the data stored in the file. e.g. for image Data (Gotthard)
1112 +
1201 1201  \\
1202 1202  
1115 +(% class="code" %)
1116 +(((
1117 +Start_event= 500 ; % define the first 10 Hz event
1118 + Number_of_events = 20; % how many 10 Hz events to load
1119 +)))
1120 +
1121 +(% style="color: rgb(0,128,0);" %)% read only part of the data:
1122 +
1123 +(% class="code" %)
1124 +(((
1125 +Gotthard_data=h5read(hdf5file,'/Experiment/Gotthard1/BL.0',[2 650 Start_event],[50 85 Number_of_events]);
1126 +)))
1127 +
1128 +(% style="color: rgb(0,128,0);" %)% start stop increment "manual" for 2 D data : [start bunch number in Gotthard data start pixelin spectrum start sample in 10 Hz trains], % [number of bunches in the Gotthard data number of points in the spectrum number of spectra ]
1129 +
1130 +(% class="code" %)
1131 +(((
1132 +VLS_Spectrum=h5read(hdf5file,'/Photon Diagnostic/Wavelength/VLS online spectrometer/PCO.ROI.X',[400 Start_event],[200 Number_of_events] );
1133 +
1134 +)))
1135 +
1136 +(% style="color: rgb(0,128,0);" %)% start stop increment "manual" for 1D data : [start sample in the spectrum start sample in 10 Hz trains],[number of points in the spectrum number of spectra ]
1137 +
1138 +(% style="color: rgb(0,128,0);" %)%GMD data
1139 +
1140 +(% class="code" %)
1141 +(((
1142 +GMD_Spectrum=h5read(hdf5file,'/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA',[1 Start_event],[40 Number_of_events] );
1143 +)))
1144 +
1145 +[[Contents>>doc:||anchor="Contents"]]
1146 +
1203 1203  \\
1148 +
1149 +== HDF5 and DOOCS ==
1150 +
1151 +Here is an outdated [[list with the available properties that are always saved (PBD) for FLASH1 as>>attach:FLASH1__DaqChannel2HdfNamePbd.xlsx]] HDF5 names and the corresponding DOOCS names
1152 +
1153 +[[Contents>>doc:||anchor="Contents"]]