Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2025/02/06 10:55
From version 4.1
edited by sendels
on 2019/08/09 12:45
Change comment: added links
To version 3.1
edited by sndueste
on 2019/08/06 15:06
Change comment: There is no comment for this version

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Author
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1 -XWiki.sendels
1 +XWiki.sndueste
Content
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2 2  
3 3  \\
4 4  
5 -* [[General information about HDF5>>doc:||anchor="General information about HDF5"]]
6 -* [[FLASH HDF5 structure>>doc:||anchor="FLASH HDF5 structure"]]
7 -* [[Most popular FLASH parameters and their names in HDF5>>doc:||anchor="Most popular FLASH parameters and their names in HDF5"]]
8 -** [[FLASH1>>doc:||anchor="FLASH1"]]
9 -*** [[Beamline info (FLASH1)>>doc:||anchor="Beamline info (FLASH1)"]]
10 -*** [[Photon Diagnostics SASE / Spectrometer (FLASH1)>>doc:||anchor="Photon Diagnostics SASE / Spectrometer (FLASH1)"]]
11 -*** [[Electron Beam properties (FLASH1)>>doc:||anchor="Electron Beam properties (FLASH1)"]]
12 -*** [[Timing information, rep rate etc.(FLASH1)>>doc:||anchor="Timing information, rep rate etc.(FLASH1)"]]
13 -*** [[Pump Probe Laser (FLASH1)>>doc:||anchor="Pump Probe Laser (FLASH1)"]]
14 -*** [[User Data (FLASH1)>>doc:||anchor="User Data (FLASH1)"]]
15 -** [[FLASH2>>doc:||anchor="FLASH2"]]
16 -** [[HDF5 structure revisions>>doc:||anchor="HDF5 structure revisions"]]
17 -* [[Example code showing how to access HDF5 files>>doc:||anchor="Example code showing how to access HDF5 files"]]
18 -** [[Samples how to read HDF5 with Matlab>>doc:||anchor="Samples how to read HDF5 with Matlab"]]
19 -** [[How to read HDF5 with Python via FLASHH5>>doc:||anchor="How to read HDF5 with Python via FLASHH5"]]
20 -* [[HDF5 and DOOCS>>doc:||anchor="HDF5 and DOOCS"]]
5 +* General information about HDF5
6 +* FLASH HDF5 structure
7 +* Most popular FLASH parameters and their names in HDF5
8 +** FLASH1
9 +*** Beamline info (FLASH1)
10 +*** Photon Diagnostics: SASE / Spectrometer (FLASH1)
11 +*** Electron Beam properties (FLASH1)
12 +*** Timing information, rep rate etc.(FLASH1)
13 +*** Pump Probe Laser (FLASH1)
14 +*** User Data (FLASH1)
15 +** FLASH2
16 +** HDF5 structure revisions
17 +* Example code showing how to access HDF5 files
18 +** Samples how to read HDF5 with Matlab
19 +** How to read HDF5 with Python via FLASHH5
20 +* HDF5 and DOOCS
21 21  
22 22  \\
23 23  
... ... @@ -33,7 +33,7 @@
33 33  {{code language="none"}}> module load xray{{/code}}
34 34  {{code language="none"}}> hdfview{{/code}}
35 35  
36 -[[Contents>>doc:||anchor="Contents"]]
36 +\\
37 37  
38 38  == FLASH HDF5 structure ==
39 39  
... ... @@ -44,12 +44,12 @@
44 44  * Beamlines
45 45  * Experiment
46 46  * Timing
47 -[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure.jpg~|~|alt="HDF5_structure.jpg" width="700" height="500"~]~]>>attach:HDF5_structure.jpg]]
47 +[[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure.jpg||alt="HDF5_structure.jpg" width="700" height="500"]]
48 48  
49 49  A detailled description of (most) channels can be found in the lower part of the hdf5 viewer:
50 -[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure_desc.jpg~|~|alt="HDF5_structure_desc.jpg" width="341" height="413"~]~]>>attach:HDF5_structure_desc.jpg]]
50 +[[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure_desc.jpg||alt="HDF5_structure_desc.jpg" width="341" height="413"]]
51 51  
52 -[[Contents>>doc:||anchor="Contents"]]
52 +\\
53 53  
54 54  \\
55 55  
... ... @@ -96,7 +96,7 @@
96 96  //always saved (PBD)//
97 97  DOOCS prop : {{code language="none"}}TTF2.FEL/BLFILTERS1/FILTER1/FW.MOTOR.POS{{/code}}
98 98  DAQ channel: {{code language="none"}}TTF2.FEL/BLFILTERS1/FILTER1/FW.MOTOR.POS{{/code}}
99 -desc: Position of the BL filterwheel 1 - to correlate with the filter material please look [[here>>doc:FLASH.Filter history (BL filterwheel 12)]]
99 +desc: Position of the BL filterwheel 1 - to correlate with the filter material please look [[here>>doc:FLASHUSER.Filter history (BL filterwheel 12)]]
100 100  units: degree
101 101  \\
102 102  
... ... @@ -104,7 +104,7 @@
104 104  //always saved (PBD)//
105 105  DOOCS prop : {{code language="none"}}TTF2.FEL/BLFILTERS2/FILTER2/FW.MOTOR.POS{{/code}}
106 106  DAQ channel: {{code language="none"}}TTF2.FEL/BLFILTERS2/FILTER2/FW.MOTOR.POS{{/code}}
107 -desc: Position of the BL filterwheel 2 - to correlate with the filter material please look [[here>>doc:FLASH.Filter history (BL filterwheel 12)]]
107 +desc: Position of the BL filterwheel 2 - to correlate with the filter material please look [[here>>doc:FLASHUSER.Filter history (BL filterwheel 12)]]
108 108  units: degree
109 109  \\
110 110  
... ... @@ -132,9 +132,9 @@
132 132  units: degree
133 133  \\
134 134  
135 -[[Contents>>doc:||anchor="Contents"]]
135 +\\
136 136  
137 -==== Photon Diagnostics SASE / Spectrometer (FLASH1) ====
137 +==== Photon Diagnostics: SASE / Spectrometer (FLASH1) ====
138 138  
139 139  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
140 140  //always saved (PBD)//
... ... @@ -148,7 +148,7 @@
148 148  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT34/VAL{{/code}}
149 149  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.USER{{/code}}
150 150  desc :Energy per pulse Tunnel (from e-) - the values are set to "0" if there was no SASE beam in the FEL
151 -units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>doc:FLASH.Calibrating the pulse resolved (electron) data from GMD]]
151 +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]]
152 152  
153 153  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel (raw){{/code}}
154 154  //always saved (PBD)//
... ... @@ -155,7 +155,7 @@
155 155  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT14/VAL{{/code}}
156 156  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.FF{{/code}}
157 157  desc :Energy per pulse Tunnel (from e-) - uncorrected values. There are also values saved if there was no beam ... just background noise
158 -units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>doc:FLASH.Calibrating the pulse resolved (electron) data from GMD]]
158 +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]]
159 159  
160 160  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy BDA{{/code}}
161 161  //always saved (PBD)//
... ... @@ -169,7 +169,7 @@
169 169  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT35/VAL{{/code}}
170 170  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.USER{{/code}}
171 171  desc :Energy per pulse BDA (from e-) - the values are set to "0" if there was no SASE beam in the FEL
172 -units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>doc:FLASH.Calibrating the pulse resolved (electron) data from GMD]]
172 +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]]
173 173  
174 174  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA (raw){{/code}}
175 175  //always saved (PBD)//
... ... @@ -176,13 +176,13 @@
176 176  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT15/VAL{{/code}}
177 177  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.FF{{/code}}
178 178  desc :Energy per pulse BDA (from e-) - uncorrected values. There are also values saved if there was no beam ... just background noise
179 -units : a.u. (more or less µJ but need to be calibrated with the "Average energy" for good precision) [[see here for help>>doc:FLASH.Calibrating the pulse resolved (electron) data from GMD]]
179 +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]]
180 180  
181 181  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA horizontal{{/code}}
182 182  //always saved (PBD)//
183 183  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
184 184  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
185 -desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (BDA, x=horizontal)
185 +desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASHUSER.Gas Monitor Detector]] (BDA, x=horizontal)
186 186  units : mm
187 187  
188 188  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA vertical{{/code}}
... ... @@ -189,7 +189,7 @@
189 189  //always saved (PBD)//
190 190  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IY.POS{{/code}}
191 191  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IY.POS{{/code}}
192 -desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (BDA, y=vertical)
192 +desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASHUSER.Gas Monitor Detector]] (BDA, y=vertical)
193 193  units : mm
194 194  
195 195  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position tunnel horizontal{{/code}}
... ... @@ -196,7 +196,7 @@
196 196  //always saved (PBD)//
197 197  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IX.POS{{/code}}
198 198  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IX.POS{{/code}}
199 -desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (TUNNEL, x=horizontal)
199 +desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASHUSER.Gas Monitor Detector]] (TUNNEL, x=horizontal)
200 200  units : mm
201 201  
202 202  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position tunnel vertical{{/code}}
... ... @@ -203,7 +203,7 @@
203 203  //always saved (PBD)//
204 204  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IY.POS{{/code}}
205 205  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IY.POS{{/code}}
206 -desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (TUNNEL, y=vertical)
206 +desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASHUSER.Gas Monitor Detector]] (TUNNEL, y=vertical)
207 207  units : mm
208 208  
209 209  {{code language="none"}}/FL1/Photon Diagnostic/Wavelength/Tunnelspectrometer/wavelength{{/code}}
... ... @@ -269,7 +269,7 @@
269 269  desc : increment value (in nm) for each pixel for the wavelength axis of the XUV Spectrum measured with the "PG spectrometer"
270 270  units : nm
271 271  
272 -[[Contents>>doc:||anchor="Contents"]]
272 +\\
273 273  
274 274  ==== Electron Beam properties (FLASH1) ====
275 275  
... ... @@ -355,7 +355,7 @@
355 355  units: nm
356 356  \\
357 357  
358 -[[Contents>>doc:||anchor="Contents"]]
358 +\\
359 359  
360 360  \\
361 361  
... ... @@ -436,7 +436,7 @@
436 436  third column: Train ID of FLASH
437 437  \\
438 438  
439 -[[Contents>>doc:||anchor="Contents"]]
439 +\\
440 440  
441 441  \\
442 442  
... ... @@ -478,7 +478,7 @@
478 478  
479 479  \\
480 480  
481 -[[Contents>>doc:||anchor="Contents"]]
481 +\\
482 482  
483 483  \\
484 484  
... ... @@ -528,7 +528,7 @@
528 528  
529 529  \\
530 530  
531 -[[Contents>>doc:||anchor="Contents"]]
531 +\\
532 532  
533 533  === FLASH2 ===
534 534  
... ... @@ -536,9 +536,9 @@
536 536  
537 537  (% class="wrapped" %)
538 538  |=(((
539 -DAQ name
539 +[[DAQ name>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main?sortcol=0;table=1;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
540 540  )))|=(((
541 -HDF5 name
541 +[[HDF5 name>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main?sortcol=1;table=1;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
542 542  )))
543 543  |(((
544 544  FLASH.UTIL/FL2.UND.MOTOR/FL2SASE3/GAP
... ... @@ -723,7 +723,7 @@
723 723  
724 724  \\
725 725  
726 -[[Contents>>doc:||anchor="Contents"]]
726 +\\
727 727  
728 728  === HDF5 structure revisions ===
729 729  
... ... @@ -739,9 +739,9 @@
739 739  
740 740  (% class="wrapped" %)
741 741  |=(((
742 -earlier HDF path (vers. 0.2)
742 +[[earlier HDF path (vers. 0.2)>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main?sortcol=0;table=2;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
743 743  )))|=(((
744 -is now (vers. 0.3)
744 +[[is now (vers. 0.3)>>url:http://hasfweb.desy.de/bin/view/Setup/HDF5main?sortcol=1;table=2;up=0#sorted_table||title="Sort by this column" rel="nofollow" shape="rect"]]
745 745  )))
746 746  |(((
747 747  /Photon Diagnostic/GMD/Beam position/position BDA x
... ... @@ -836,7 +836,7 @@
836 836  
837 837  \\
838 838  
839 -[[Contents>>doc:||anchor="Contents"]]
839 +\\
840 840  
841 841  \\
842 842  
... ... @@ -895,7 +895,7 @@
895 895  GMD_Spectrum=h5read(hdf5file,'/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA',[1 Start_event],[40 Number_of_events] );
896 896  )))
897 897  
898 -[[Contents>>doc:||anchor="Contents"]]
898 +\\
899 899  
900 900  === How to read HDF5 with Python via FLASHH5 ===
901 901  
... ... @@ -906,5 +906,3 @@
906 906  == HDF5 and DOOCS ==
907 907  
908 908  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
909 -
910 -[[Contents>>doc:||anchor="Contents"]]