Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2025/02/06 10:55
From version 28.1
edited by sndueste
on 2019/10/22 08:53
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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
... ... @@ -27,43 +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"]] [[download HDF5 (Images)>>url:https://desycloud.desy.de/index.php/s/nyEgeCWJFC4gao2||shape="rect"]]
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 49  \\
50 50  
51 51  \\
52 52  
53 -[[download HDF5 (GHz ADC and OPIS)>>url:https://desycloud.desy.de/index.php/s/AeA2kPNNnZgX95A||shape="rect"]]
53 +[[Contents>>doc:||anchor="Contents"]]
54 54  
55 55  \\
56 56  
57 -\\
57 +== The new (starting 2021) HDF5 format ==
58 58  
59 -[[Contents>>doc:||anchor="Contents"]]
59 +Here is some documentation on the changes of the HDF5 format that well be avaliable in 2021 (work in progress)
60 60  
61 61  \\
62 62  
63 63  \\
64 64  
65 -== 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 ==
66 66  
67 +{{id name="DOOCSparameters"/}}
68 +
67 67  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"]].
68 68  The most common and often used ones are summarized below:
69 69  
... ... @@ -143,7 +143,7 @@
143 143  \\
144 144  
145 145  
146 -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
147 147  
148 148  [[Contents>>doc:||anchor="Contents"]]
149 149  
... ... @@ -153,13 +153,20 @@
153 153  
154 154  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
155 155  //always saved (PBD)//
156 -DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT04/VAL{{/code}}
157 -DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENPULSEIC{{/code}}
158 -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)
159 159  units : microJ
160 160  
161 161  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
162 -//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 +
163 163  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT34/VAL{{/code}}
164 164  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.USER{{/code}}
165 165  desc :Energy per pulse Tunnel (from e-) - the values are set to "0" if there was no SASE beam in the FEL
... ... @@ -173,7 +173,11 @@
173 173  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]]**
174 174  
175 175  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy BDA{{/code}}
176 -//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 +
177 177  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT05/VAL{{/code}}
178 178  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENPULSEIC{{/code}}
179 179  desc : calibrated average SASE Energy/pulse measured in the BDA (in the experimental hall) after the attenuator (ion current)
... ... @@ -180,7 +180,10 @@
180 180  units : microJ
181 181  
182 182  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA{{/code}}
183 -//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}}(%%)
184 184  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT35/VAL{{/code}}
185 185  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.USER{{/code}}
186 186  desc :Energy per pulse BDA (from e-) - the values are set to "0" if there was no SASE beam in the FEL
... ... @@ -193,6 +193,8 @@
193 193  desc :Energy per pulse BDA (from e-) - uncorrected values. There are also values saved if there was no beam ... just background noise
194 194  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]]**
195 195  
212 +\\
213 +
196 196  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA horizontal{{/code}}
197 197  //always saved (PBD)//
198 198  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
... ... @@ -304,10 +304,25 @@
304 304  //always saved (PBD)//
305 305  DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/4DBC3/LOW_CHARGE_ARRIVAL_TIME{{/code}}
306 306  DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/4DBC3.LOW_CHARGE_ARRIVAL_TIME{{/code}}
307 -desc: Electron bunch arrival time measured with the BAM (more or less) before the undulator (pulse resolved data)
308 -units: ps (bigger numbers indicate later arrivaltime of the electrons)
309 -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)
310 310  
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 +
311 311  ===== electron beam profile =====
312 312  
313 313  {{code language="none"}}/FL1/Electron Diagnostic/Electron bunch profile/TDS profile{{/code}}
... ... @@ -749,17 +749,30 @@
749 749  =====
750 750  arrival time =====
751 751  
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 +
752 752  **FL1**{{code language="none"}}//Electron Diagnostic/BAM/4DBC3/electron bunch arrival time (low charge){{/code}}
753 753  //always saved (PBD2)//
754 754  DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/4DBC3/LOW_CHARGE_ARRIVAL_TIME{{/code}}
755 755  DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/4DBC3.LOW_CHARGE_ARRIVAL_TIME{{/code}}
756 -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)
757 757  units: ps (bigger numbers indicate later arrivaltime of the electrons)
758 758  
759 -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.
760 -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 +\\
761 761  
762 -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}}
763 763  
764 764  
765 765  [[Contents>>doc:||anchor="Contents"]]