Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2025/02/06 10:55
From version 40.1
edited by sndueste
on 2021/02/09 14:35
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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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... ... @@ -18,56 +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 -\\
48 -
49 -ADC data as example for **fast** **data** (10 Hz):
50 -
51 -\\
52 -
53 -[[image:attach:image2020-11-16_15-26-28.png||height="250"]]
54 -
55 -\\
56 -
57 -{{info title="Sample scripts in python"}}
58 -== Reference implementation (Python) ==
59 -
60 -[[~[~[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"]]
61 -
62 -(% class="Object" %)[[https:~~/~~/gitlab.desy.de/christopher.passow/flash-daq-hdf>>url:https://gitlab.desy.de/christopher.passow/flash-daq-hdf||shape="rect"]]
63 -{{/info}}
64 -
65 -\\
66 -
67 -\\
68 -
69 -== The discontinued (till 2021) FLASH HDF5 structure ==
70 -
71 71  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:
72 72  
73 73  * Electron Diagnostic
... ... @@ -102,6 +102,14 @@
102 102  
103 103  \\
104 104  
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 +
105 105  == Most popular FLASH parameters and their names in HDF5, DOOCS and (raw) DAQ ==
106 106  
107 107  {{id name="DOOCSparameters"/}}
... ... @@ -191,14 +191,12 @@
191 191  
192 192  \\
193 193  
194 -==== 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) ====
195 195  
196 -\\
197 -
198 -(% style="color: rgb(0,0,0);" %)**Discontinued GMD data recording / evaluation  (VME + PhotonFlux ML server)**
199 -
200 200  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
201 -//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}}
202 202  
203 203  (% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT04/VAL{{/code}} (%%)
204 204  (% style="color: rgb(0,0,0);" %)DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENPULSEIC{{/code}}(%%)
... ... @@ -208,6 +208,9 @@
208 208  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
209 209  //always saved (PBD)//
210 210  
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 +
211 211  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT34/VAL{{/code}}
212 212  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.USER{{/code}}
213 213  desc :Energy per pulse Tunnel (from e-) - the values are set to "0" if there was no SASE beam in the FEL
... ... @@ -223,6 +223,9 @@
223 223  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy BDA{{/code}}
224 224  //always saved (PBD)//
225 225  
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 +
226 226  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT05/VAL{{/code}}
227 227  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENPULSEIC{{/code}}
228 228  desc : calibrated average SASE Energy/pulse measured in the BDA (in the experimental hall) after the attenuator (ion current)
... ... @@ -231,6 +231,8 @@
231 231  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA{{/code}}
232 232  //always saved (PBD)//
233 233  
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}}(%%)
234 234  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT35/VAL{{/code}}
235 235  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.USER{{/code}}
236 236  desc :Energy per pulse BDA (from e-) - the values are set to "0" if there was no SASE beam in the FEL
... ... @@ -245,55 +245,6 @@
245 245  
246 246  \\
247 247  
248 -(% style="color: rgb(0,0,0);" %)**NEW (2021) GMD data recording / evaluation  (MTCA, analog to FLASH2 and XFEL)**
249 -
250 -{{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
251 -//always saved (PBD)//
252 -(% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}} (%%)
253 -(% style="color: rgb(0,0,0);" %)DAQ channel: {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}}
254 -
255 -desc : calibrated average SASE Energy/pulse measured in the TUNNEL upstream the gas attenuator
256 -units : microJ
257 -
258 -\\
259 -
260 -{{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
261 -//always saved (PBD)//
262 -
263 -(% style="color: rgb(0,0,0);" %)DOOCS prop : 
264 -{{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}}
265 -
266 -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)
267 -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]]**
268 -
269 -{{info title="GMD pulse resolved data structure"}}
270 -For every pulse in the pulse train the information is saved:
271 -
272 -
273 -1. **Intensity per pulse** (a.u. (more or less µJ ))
274 -1. Intensity per pulse (auxillary GMD) - not used
275 -1. Position horizontal (mm, for a single pulse the position information may be very noisy  - talk to your local contact)
276 -1. Position vertical (mm, for a single pulse the position information may be very noisy  - talk to your local contact)
277 -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)(%%))
278 -1. Position horizontal sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
279 -1. Position vertical sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
280 -1. Combined warning and error flags
281 -
282 -The pulse energy and the error are plotted for the first bunch of the pulse trains saved in this 
283 -file
284 -
285 -
286 -[[image:attach:image2021-2-9_10-51-6.png||height="250"]]
287 -
288 -\\
289 -{{/info}}
290 -
291 -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 !
292 -
293 -\\
294 -
295 -Besides  pulse energy the GMD also provides information about the beam position
296 -
297 297  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA horizontal{{/code}}
298 298  //always saved (PBD)//
299 299  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
... ... @@ -322,10 +322,6 @@
322 322  desc :Beam position of the photon Beam determined by the GMD (TUNNEL, y=vertical)
323 323  units : mm
324 324  
325 -\\
326 -
327 -==== Spectrometer (FLASH1) ====
328 -
329 329  {{code language="none"}}/FL1/Photon Diagnostic/Wavelength/Tunnelspectrometer/wavelength{{/code}}
330 330  _always saved (when Spectrum is measured !!) (PBD) _
331 331  DOOCS prop : {{code language="none"}}TTF2.EXP/PHOTONWL.ML/WAVE_LENGTH/VAL.TD{{/code}}
... ... @@ -456,7 +456,7 @@
456 456  ===== electron bunch energy =====
457 457  
458 458  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/average electron energy{{/code}}
459 -//always saved (PBD)//
372 +_always saved (PBD)
460 460  DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/E_INTRA_MEAN/VAL{{/code}}
461 461  DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/E_MEAN{{/code}}
462 462  desc: electron bunch energy (average over the bunch train)
... ... @@ -464,7 +464,7 @@
464 464  \\
465 465  
466 466  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/pulse resolved energy{{/code}}
467 -//always saved (PBD)//
380 +_always saved (PBD)
468 468  DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/E_SPECT/VAL.TD{{/code}}
469 469  DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/E_SPECT{{/code}}
470 470  desc: electron bunch energy bunch resolved
... ... @@ -473,7 +473,7 @@
473 473  \\
474 474  
475 475  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/wavelength bunch train average{{/code}}
476 -//always saved (PBD)//
389 +_always saved (PBD)
477 477  DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/LAMBDA_MEAN/VAL{{/code}}
478 478  DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/LAMBDA_MEAN{{/code}}
479 479  desc: Wavelength calculated by the electron bunch energy (average over the bunch train) (FLASH1)
... ... @@ -667,12 +667,12 @@
667 667  
668 668  ==== Beamline info (FLASH2) ====
669 669  
670 -{{code language="none"}}/FL2/Beamlines/Attenuator/pressure  {{/code}}
671 -(% style="color: rgb(0,0,0);" %)//always saved (PBD2)// (%%)
672 -(% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
673 -(% style="color: rgb(0,0,0);" %)DAQ channel:  {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
674 -(% style="color: rgb(0,0,0);" %)desc: set pressure in the gas attenuator (%%)
675 -(% 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(%%)
676 676  \\
677 677  
678 678  {{code language="none"}}/FL2/Beamlines/FL20/Shutter/open{{/code}}
... ... @@ -691,13 +691,11 @@
691 691  units: degree
692 692  \\
693 693  
694 -/FL2/Beamlines/Filter wheel/position wheel 2
695 -always saved (PBD2)
696 -DOOCS prop : {{code language="none"}}FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS{{/code}}
697 -DAQ channel: {{code language="none"}}FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS{{/code}}
698 -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]]
699 -units: degree
700 700  
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 +
701 701  \\
702 702  
703 703  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
... ... @@ -726,14 +726,13 @@
726 726  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)
727 727  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]]**
728 728  
729 -{{info title="GMD pulse resolved data structure"}}
730 730  For every pulse in the pulse train the information is saved:
731 731  
732 732  
733 733  1. **Intensity per pulse** (a.u. (more or less µJ ))
734 734  1. Intensity per pulse (auxillary GMD) - not used
735 -1. Position horizontal (mm, for a single pulse the position information may be very noisy  - talk to your local contact)
736 -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)
737 737  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)(%%))
738 738  1. Position horizontal sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
739 739  1. Position vertical sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
... ... @@ -745,10 +745,8 @@
745 745  
746 746  [[image:attach:image2021-2-9_10-51-6.png||height="250"]]
747 747  
748 -\\
749 -{{/info}}
750 750  
751 -\\
659 +{{code language="none"}}{{/code}}
752 752  
753 753  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 !
754 754  
... ... @@ -776,15 +776,13 @@
776 776  
777 777  \\
778 778  
779 -/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position tunnel x
780 -always saved (PBD2)
781 -DOOCS prop : FLASH.FEL/XGM.BPM/FL2.HALL/X.TD
782 -DAQ channel: FLASH.FEL/XGM.BPM/FL2.HALL:2
783 -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 ...)
784 -units : mm   
785 785  
786 -(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}}
787 787  
692 +{{code language="none"}}(x=horizontal, y = vertial){{/code}}
693 +
788 788  again the same parameter set is available for the **HALL GMD**
789 789  
790 790  \\
... ... @@ -1185,6 +1185,61 @@
1185 1185  
1186 1186  \\
1187 1187  
1094 +=== Samples how to read HDF5 with Matlab ===
1095 +
1096 +The examples apply to HDF files with HDF tree version before vers. 0.3.0.
1097 +
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
1099 +
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
1101 +
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 +
1113 +\\
1114 +
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 +
1147 +\\
1148 +
1188 1188  == HDF5 and DOOCS ==
1189 1189  
1190 1190  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