Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2025/02/06 10:55
From version 37.1
edited by cpassow
on 2020/11/23 16:26
Change comment: There is no comment for this version
To version 33.1
edited by sndueste
on 2020/10/28 11:26
Change comment: There is no comment for this version

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1 -XWiki.cpassow
1 +XWiki.sndueste
Content
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8 8  
9 9  == General information about HDF5 ==
10 10  
11 -HDF5 is a data format maintained by the HDF group. For detailed general information see [[here~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://portal.hdfgroup.org/display/support||shape="rect"]]
11 +HDF5 is a data format maintained by the HDF group. For detailed general information see [[here~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://www.hdfgroup.org/HDF5/||shape="rect"]]
12 12  
13 -To download the HDF5 Viewer click [[here~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://portal.hdfgroup.org/display/support/Download+HDFView||shape="rect"]]
13 +To download the HDF5 Viewer click [[here~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://support.hdfgroup.org/products/java/hdfview/index.html||shape="rect"]]
14 14  
15 15  For use on the DESY Maxwell or PAL (max-fsc or pal) **hdfview** is available in the xray module :
16 16  {{code language="none"}}> module load xray{{/code}}
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18 18  
19 19  [[Contents>>doc:||anchor="Contents"]]
20 20  
21 -== The current FLASH HDF5 structure ==
21 +== FLASH HDF5 structure ==
22 22  
23 -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:
23 +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 organised according to train IDs. The general structure is:
24 24  
25 25  * Electron Diagnostic
26 26  * Photon Diagnostics
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27 27  * Beamlines
28 28  * Experiment
29 29  * Timing
30 -[[image:attach:HDF5_structure.jpg||height="400"]]
30 +[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure.jpg~|~|alt="HDF5_structure.jpg" width="700" height="500"~]~]>>attach:HDF5_structure.jpg]]
31 31  
32 -A detailed description of (most) channels can be found in the lower part of the hdf5 viewer:
33 -[[image:attach:HDF5_structure_desc.jpg||thumbnail="true" height="250"]]
32 +A detailled description of (most) channels can be found in the lower part of the hdf5 viewer:
33 +[[~[~[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]]
34 34  
35 35  [[Contents>>doc:||anchor="Contents"]]
36 36  
37 37  \\
38 38  
39 -=== HDF5 example files ===
39 +== HDF5 example files ==
40 40  
41 41  Here we have a few HDF5 samples (User data combined with Photon diagnostics data) from a few beamtimes showing the different kind options.
42 42  
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54 54  
55 55  \\
56 56  
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 61  \\
62 62  
63 -\\
64 -
65 65  == Most popular FLASH parameters and their names in HDF5, DOOCS and (raw) DAQ ==
66 66  
67 67  {{id name="DOOCSparameters"/}}
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145 145  \\
146 146  
147 147  
148 -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
142 +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
149 149  
150 150  [[Contents>>doc:||anchor="Contents"]]
151 151  
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155 155  
156 156  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
157 157  //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}}
160 -
161 -(% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT04/VAL{{/code}} (%%)
162 -(% style="color: rgb(0,0,0);" %)DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENPULSEIC{{/code}}(%%)
163 -desc : calibrated average SASE Energy/pulse measured in the TUNNEL upstream the gas attenuator (ion current)
152 +DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT04/VAL{{/code}}
153 +DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENPULSEIC{{/code}}
154 +desc : calibrated average SASE Energy/pulse measured in the TUNNEL before the attenuator (ion current)
164 164  units : microJ
165 165  
166 166  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
167 -//always saved (PBD)//
168 -
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 -
158 +//always saved (PBD)//
172 172  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT34/VAL{{/code}}
173 173  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.USER{{/code}}
174 174  desc :Energy per pulse Tunnel (from e-) - the values are set to "0" if there was no SASE beam in the FEL
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182 182  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]]**
183 183  
184 184  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy BDA{{/code}}
185 -//always saved (PBD)//
186 -
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 -
172 +//always saved (PBD)//
190 190  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT05/VAL{{/code}}
191 191  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENPULSEIC{{/code}}
192 192  desc : calibrated average SASE Energy/pulse measured in the BDA (in the experimental hall) after the attenuator (ion current)
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193 193  units : microJ
194 194  
195 195  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA{{/code}}
196 -//always saved (PBD)//
197 -
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}}(%%)
179 +//always saved (PBD)//
200 200  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT35/VAL{{/code}}
201 201  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.USER{{/code}}
202 202  desc :Energy per pulse BDA (from e-) - the values are set to "0" if there was no SASE beam in the FEL
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209 209  desc :Energy per pulse BDA (from e-) - uncorrected values. There are also values saved if there was no beam ... just background noise
210 210  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]]**
211 211  
212 -\\
213 -
214 214  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA horizontal{{/code}}
215 215  //always saved (PBD)//
216 216  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
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1150 1150  
1151 1151  [[Contents>>doc:||anchor="Contents"]]
1152 1152  
1131 +=== How to read HDF5 with Python via FLASHH5 ===
1132 +
1133 +With [[FlashH5>>doc:FLASHUSER.FLASHH5 for easier access of FLASH's HDF5 files]] we provide h5py based examples to access and evaluate FLASH's HDF5 files.
1134 +
1153 1153  \\
1154 1154  
1155 1155  == HDF5 and DOOCS ==