Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2025/02/06 10:55
From version 27.1
edited by sndueste
on 2019/10/21 17:34
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To version 35.1
edited by sndueste
on 2020/11/16 10:19
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... ... @@ -8,9 +8,9 @@
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://www.hdfgroup.org/HDF5/||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://portal.hdfgroup.org/display/support||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://support.hdfgroup.org/products/java/hdfview/index.html||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://portal.hdfgroup.org/display/support/Download+HDFView||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}}
... ... @@ -18,9 +18,9 @@
18 18  
19 19  [[Contents>>doc:||anchor="Contents"]]
20 20  
21 -== FLASH HDF5 structure ==
21 +== The current 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 organised 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 organized according to train IDs. The general structure is:
24 24  
25 25  * Electron Diagnostic
26 26  * Photon Diagnostics
... ... @@ -27,41 +27,45 @@
27 27  * Beamlines
28 28  * Experiment
29 29  * Timing
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]]
30 +[[image:attach:HDF5_structure.jpg||height="400"]]
31 31  
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]]
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"]]
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  
43 -Example 1:  Images saved at FLASH2
43 +[[image:attach:image2019-10-21_17-2-50.png||thumbnail="true" width="300"]] [[download HDF5 (Images @ FL2)>>url:https://desycloud.desy.de/index.php/s/nyEgeCWJFC4gao2||shape="rect"]]
44 44  
45 45  \\
46 46  
47 -[[image:attach:image2019-10-21_17-2-50.png||thumbnail="true" height="150"]]
47 +[[~[~[image:attach:image2019-10-22_10-52-27.png~|~|thumbnail="true" width="300"~]~]download HDF5 (GHz ADC and OPIS @ FL2)>>url:https://desycloud.desy.de/index.php/s/AeA2kPNNnZgX95A||shape="rect"]]
48 48  
49 -[[download HDF5>>url:https://desycloud.desy.de/index.php/s/nyEgeCWJFC4gao2||shape="rect"]]
50 -
51 51  \\
52 52  
53 53  \\
54 54  
53 +[[Contents>>doc:||anchor="Contents"]]
54 +
55 55  \\
56 56  
57 -[[Contents>>doc:||anchor="Contents"]]
57 +== The new (starting 2021) HDF5 format ==
58 58  
59 +Here is some documentation on the changes of the HDF5 format that well be avaliable in 2021 (work in progress)
60 +
59 59  \\
60 60  
61 61  \\
62 62  
63 -== Most popular FLASH parameters and their names in HDF5, DOOCS and (raw) DAQ ==
65 +== Most popular FLASH parameters and their names in HDF5, DOOCS and (raw) DAQ ==
64 64  
67 +{{id name="DOOCSparameters"/}}
68 +
65 65  The complete list for the relation between DOOCS names and HDF5 names for the recordable parameters can be found in [[DESY's Repository~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:https://stash.desy.de/projects/CS/repos/pah/browse/src/camp/data/channel2HdfName.dat||shape="rect"]].
66 66  The most common and often used ones are summarized below:
67 67  
... ... @@ -141,7 +141,7 @@
141 141  \\
142 142  
143 143  
144 -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
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
145 145  
146 146  [[Contents>>doc:||anchor="Contents"]]
147 147  
... ... @@ -151,13 +151,20 @@
151 151  
152 152  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
153 153  //always saved (PBD)//
154 -DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT04/VAL{{/code}}
155 -DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENPULSEIC{{/code}}
156 -desc : calibrated average SASE Energy/pulse measured in the TUNNEL before the attenuator (ion current)
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)
157 157  units : microJ
158 158  
159 159  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
160 -//always saved (PBD)//
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 +
161 161  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT34/VAL{{/code}}
162 162  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.USER{{/code}}
163 163  desc :Energy per pulse Tunnel (from e-) - the values are set to "0" if there was no SASE beam in the FEL
... ... @@ -171,7 +171,11 @@
171 171  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]]**
172 172  
173 173  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy BDA{{/code}}
174 -//always saved (PBD)//
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 +
175 175  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT05/VAL{{/code}}
176 176  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENPULSEIC{{/code}}
177 177  desc : calibrated average SASE Energy/pulse measured in the BDA (in the experimental hall) after the attenuator (ion current)
... ... @@ -178,7 +178,10 @@
178 178  units : microJ
179 179  
180 180  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA{{/code}}
181 -//always saved (PBD)//
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}}(%%)
182 182  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT35/VAL{{/code}}
183 183  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.USER{{/code}}
184 184  desc :Energy per pulse BDA (from e-) - the values are set to "0" if there was no SASE beam in the FEL
... ... @@ -191,6 +191,8 @@
191 191  desc :Energy per pulse BDA (from e-) - uncorrected values. There are also values saved if there was no beam ... just background noise
192 192  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]]**
193 193  
212 +\\
213 +
194 194  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA horizontal{{/code}}
195 195  //always saved (PBD)//
196 196  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
... ... @@ -302,10 +302,25 @@
302 302  //always saved (PBD)//
303 303  DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/4DBC3/LOW_CHARGE_ARRIVAL_TIME{{/code}}
304 304  DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/4DBC3.LOW_CHARGE_ARRIVAL_TIME{{/code}}
305 -desc: Electron bunch arrival time measured with the BAM (more or less) before the undulator (pulse resolved data)
306 -units: ps (bigger numbers indicate later arrivaltime of the electrons)
307 -note: besides the arivaltime from FLASH1 there is also the FLASH2/3 electron arrival time saved. [[LINK to detailled infos from MSK (may only work inside DESY network~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://www.desy.de/~~mbock/pages/BAM_daq_channel_descriptions.html||shape="rect"]] and to a recent  [[talk about the working principle of the BAM>>attach:BAM-basics and outlook-2018_DESY-template_16-9Format.pdf]]
325 +desc: Electron bunch arrival time measured with the BAM inside the accelerator - however shows a very good correlation to the arrivaltime  of the XUV pulses in the experiment (pulse resolved data).
326 +units: ps (bigger numbers indicate later arrivaltime of the electrons)
308 308  
328 +{{code language="none"}}/FL1/Electron Diagnostic/BAM/1SFELC/electron bunch arrival time (low charge){{/code}}
329 +//always saved (PBD)//
330 +DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/1SFELC/LOW_CHARGE_ARRIVAL_TIME{{/code}}
331 +DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/1SFELC.LOW_CHARGE_ARRIVAL_TIME{{/code}}
332 +desc: Electron bunch arrival time measured with the BAM  before the undulator (pulse resolved data). This one was newly installed in 2020.
333 +units: ps (bigger numbers indicate later arrivaltime of the electrons)
334 +
335 +{{info title="BAM hints"}}
336 +* besides the arrivaltime from FLASH1 there is also the FLASH2/3 electron arrival time saved.In case of doubt ask your local contact
337 +* [[Link a collection of papers related to the BAM and the analysis of pump-probe experiments >>doc:FLASHUSER.Additional helpful things.FLASH beamlines and instruments references.WebHome]]
338 +* [[LINK to detailed infos from MSK (may only work inside DESY network~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://www.desy.de/~~mbock/pages/BAM_daq_channel_descriptions.html||shape="rect"]]
339 +* a recent  [[talk about the working principle of the BAM>>attach:BAM-basics and outlook-2018_DESY-template_16-9Format.pdf]]
340 +{{/info}}
341 +
342 +\\
343 +
309 309  ===== electron beam profile =====
310 310  
311 311  {{code language="none"}}/FL1/Electron Diagnostic/Electron bunch profile/TDS profile{{/code}}
... ... @@ -747,17 +747,30 @@
747 747  =====
748 748  arrival time =====
749 749  
785 +{{code language="none"}}/FL2/Electron Diagnostic/BAM/8FL2XTDS/electron bunch arrival time (low charge){{/code}}
786 +//always saved (PBD2)//
787 +DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/8FL2XTDS/LOW_CHARGE_ARRIVAL_TIME{{/code}}
788 +DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/8FL2XTDS.LOW_CHARGE_ARRIVAL_TIME{{/code}}
789 +desc: Electron bunch arrival time measured with the BAM after the FLASH2 undulator (pulse resolved data)
790 +units: ps (bigger numbers indicate later arrivaltime of the electrons)
791 +
750 750  **FL1**{{code language="none"}}//Electron Diagnostic/BAM/4DBC3/electron bunch arrival time (low charge){{/code}}
751 751  //always saved (PBD2)//
752 752  DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/4DBC3/LOW_CHARGE_ARRIVAL_TIME{{/code}}
753 753  DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/4DBC3.LOW_CHARGE_ARRIVAL_TIME{{/code}}
754 -desc: Electron bunch arrival time measured with the BAM (more or less) before the undulator (pulse resolved data)
796 +desc: Electron bunch arrival time measured with the BAM  in the accelerator  (pulse resolved data)
755 755  units: ps (bigger numbers indicate later arrivaltime of the electrons)
756 756  
757 -The BAM measures the arrivaltime of** FLASH 1 and FLASH2** in the same data set (thus also sorted in at /FL1/ !). The first values are for FLASH1 bunches.
758 -After a gap of about 70 micros ( 70 colums)  with  as entry for the switching between FLASH 1 and 2 the values for the electrons used in FLASH2 start.  The start time of FLASH2 is also recorded in the DAQ. FLASH1 start time is for historic reasons 700. thus if e.g. the start time of FLASH2 ( property name see below) is 1200 it means that FLASH starts at column 500 (1200-700) ...
799 +\\
759 759  
760 -Docu for BAM:  [[LINK to detailled infos from MSK (may only work inside DESY network~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://www.desy.de/~~mbock/pages/BAM_daq_channel_descriptions.html||shape="rect"]] and to a recent [[talk about the working principle of the BAM>>attach:BAM-basics and outlook-2018_DESY-template_16-9Format.pdf]]
801 +{{info title="BAM hints"}}
802 +* The BAM 4DBC3 measures the arrivaltime of** FLASH 1 and FLASH2** in the same data set (thus also sorted in at /FL1/ !).
803 +* The BAM 8FL2XTDS measures only for FLASH2 BUT has the same data structure as the other BAMS ... thus there are also (random) values in in the  FLASH1 time slot 
804 +** Structure: The first values are for FLASH1 bunches. After a gap of about 70 micros ( 70 colums)  with  as entry for the switching between FLASH 1 and 2 the values for the electrons used in FLASH2 start.  The start time of FLASH2 is also recorded in the DAQ. FLASH1 start time is for historic reasons 700. thus if e.g. the start time of FLASH2 ( property name see below) is 1200 it means that FLASH starts at column 500 (1200-700) ... .In case of doubt ask your local contact
805 +* [[Link a collection of papers related to the BAM and the analysis of pump-probe experiments >>doc:FLASHUSER.Additional helpful things.FLASH beamlines and instruments references.WebHome]]
806 +* [[LINK to detailed infos from MSK (may only work inside DESY network~[~[image:url:http://hasfweb.desy.de/pub/TWiki/TWikiDocGraphics/external-link.gif~|~|width="13" height="12"~]~]>>url:http://www.desy.de/~~mbock/pages/BAM_daq_channel_descriptions.html||shape="rect"]]
807 +* a recent  [[talk about the working principle of the BAM>>attach:BAM-basics and outlook-2018_DESY-template_16-9Format.pdf]]
808 +{{/info}}
761 761  
762 762  
763 763  [[Contents>>doc:||anchor="Contents"]]