Changes for page The FLASH HDF5 structure

Last modified by sndueste on 2025/02/06 10:55

From 45.1 to 46.1 From 58.1 to 59.1

From version 46.1

edited by sndueste
on 2021/02/10 10:13

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To version 58.1

edited by sndueste
on 2022/09/07 17:20

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@@ -19,6 +19,12 @@
  {{code language="none"}}> module load xray{{/code}}
  {{code language="none"}}> hdfview{{/code}}
++or you can use
++
++{{code language="none"}}> silx view{{/code}}
++
++\\
++
  [[Contents>>doc:||anchor="Contents"]]
  == The FLASH HDF5 format ==
@@ -32,7 +32,7 @@
  \\
  {{expand title="Discontinued HDF formats"}}
--== Comparison to FLASH's deprecated HDF formats ==
++=== Comparison to FLASH's deprecated HDF formats ===
  Before 2021, FLASH provided two different HDF formats formally known as //near-online// and //offline// HDF files.
@@ -97,12 +97,12 @@
  {{layout-section ac:type="single"}}
  {{layout-cell}}
--{{info title="Sample scripts in python"}}
++{{info}}
  === Reference implementation (Python) ===
--[[~[~[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"]]
++(imperative)  (% class="Object" %)[[https:~~/~~/gitlab.desy.de/christopher.passow/flash-daq-hdf>>url:https://gitlab.desy.de/christopher.passow/flash-daq-hdf||shape="rect"]]
--(% class="Object" %)[[https:~~/~~/gitlab.desy.de/christopher.passow/flash-daq-hdf>>url:https://gitlab.desy.de/christopher.passow/flash-daq-hdf||shape="rect"]]
++(% class="Object" %)(object oriented) [[https:~~/~~/gitlab.desy.de/christopher.passow/fdh-builder>>url:https://gitlab.desy.de/christopher.passow/fdh-builder.git||shape="rect"]]
  {{/info}}
  {{/layout-cell}}
  {{/layout-section}}
@@ -200,8 +200,7 @@
  ==== Photon Diagnostics SASE ([[GMD>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/gmd_intensity_and_position/index_eng.html||shape="rect"]]) ====
--\\
--
++{{expand title="Discontinued GMD format (used until 2021)"}}
  (% style="color: rgb(0,0,0);" %)**Discontinued GMD data recording / evaluation  (VME + PhotonFlux ML server)**
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
@@ -249,10 +249,11 @@
  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.FF{{/code}}
  desc :Energy per pulse BDA (from e-) - uncorrected values. There are also values saved if there was no beam ... just background noise
  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]]**
++{{/expand}}
  \\
--(% style="color: rgb(0,0,0);" %)**NEW (2021) GMD data recording / evaluation  (MTCA, analog to FLASH2 and XFEL)**
++(% style="letter-spacing: 0px; color: rgb(0, 0, 0)" %)**NEW (since 2021) GMD data recording / evaluation  (same format as FLASH2 and XFEL)**
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
  //always saved (PBD)//
@@ -410,8 +410,27 @@
  units: nC
  =====
--arrival time =====
++arrival time (BAM) =====
++{{info title="BAM information: updates 2022"}}
++* The data format of the BAM has been completely altered in the 2022 shutdown
++* before 2022 BAMs were always saving the arrival time information for each 1µs bucked regardless if there were electrons in the accelerator or not. IN addition the arrival times for  FL1 and FL2 were saved in the same parameter ...
++* THIS is now different. there are new parameters for pulses that go to FL1 and to FL2 (in detail: first time slot of the accelerator and second)
++* There has been also a renaming  (and relocation) of the BAMs.
++** acc:  4DBC3 → FL0.DBC2
++** FL1: 1SFELC →  FL1.SFELC
++** FL2: FL2XTDS → (% style="color: rgb(23,43,77);" %)FL2.SEED5
++* for more Info: [[LINK to detailed infos from MSK>>url:https://confluence.desy.de/display/SDiagPublic/BAM+Data+Structure||shape="rect"]]
++* [[Info collection about the BAMs and how to use the BAM data>>url:https://confluence.desy.de/display/FLASHUSER/Info+collection+for+the+BAM||shape="rect"]]
++* [[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]]
++* a recent  [[talk about the working principle of the BAM>>attach:BAM-basics and outlook-2018_DESY-template_16-9Format.pdf]]
++{{/info}}
++
++\\
++
++{{expand title="Discontinued BAM format (used until end 2021)"}}
++(% style="color: rgb(0,0,0);" %)**Discontinued BAM data recording **
++
  {{code language="none"}}/FL1/Electron Diagnostic/BAM/4DBC3/electron bunch arrival time (low charge){{/code}}
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/4DBC3/LOW_CHARGE_ARRIVAL_TIME{{/code}}
@@ -419,17 +419,70 @@
  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).
  units: ps (bigger numbers indicate later arrivaltime of the electrons)
++\\
++
  {{code language="none"}}/FL1/Electron Diagnostic/BAM/1SFELC/electron bunch arrival time (low charge){{/code}}
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/1SFELC/LOW_CHARGE_ARRIVAL_TIME{{/code}}
  DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/1SFELC.LOW_CHARGE_ARRIVAL_TIME{{/code}}
  desc: Electron bunch arrival time measured with the BAM  before the undulator (pulse resolved data). This one was newly installed in 2020.
--units: ps (bigger numbers indicate later arrivaltime of the electrons)
++units: ps (bigger numbers indicate later arrival time of the electrons)
++{{/expand}}
++(% style="color: rgb(255,102,0);" %)DBC2/electron bunch arrival time{{code language="none"}}/FL1/Electron Diagnostic/BAM/{{/code}}(%%)
++//always saved (PBD)//
++DOOCS prop : FLASH.SDIAG/BAM/FL0.DBC2/ARRIVAL_TIME.absolute.SA1
++DAQ channel: (% style="color: rgb(255,102,0);" %)FLASH.SDIAG/BAM/FL0.DBC2/ARRIVAL_TIME.absolute.SA1 (%%)
++desc: Electron bunch arrival time measured with the BAM inside the accelerator (after bunch compressor 2) - It shows a very good correlation to the arrival time  of the XUV pulses in the experiment (see help).  The SA1 indicates the data is recorded for the first time slot at FLASh, typically used for FLASH1
++units: fs (bigger numbers (typically) indicate later arrival times of the electrons).
++
++\\
++
++(% style="color: rgb(255,102,0);" %)DBC2/error{{code language="none"}}/FL1/Electron Diagnostic/BAM/{{/code}}(%%)
++//always saved (PBD)//
++DOOCS prop : FLASH.SDIAG/BAM/FL0.DBC2/ARRIVAL_TIM(% style="color: rgb(0,0,0);" %)E.bamError(%%)
++DAQ channel: (% style="color: rgb(255,102,0);" %)FLASH.SDIAG/BAM/FL0.DBC2/ARRIVAL_TIME.BAMERROR(%%)
++desc: If the value is 0 , the BAM is working well. If it is non-zero there is a problem !!
++
++\\
++
++(% style="color: rgb(255,102,0);" %)DBC2/error{{code language="none"}}/FL1/Electron Diagnostic/BAM/{{/code}}(%%)
++//always saved (PBD)//
++DOOCS prop : FLASH.SDIAG/BAM/FL0.DBC2/ARRIVAL_TIM(% style="color: rgb(0,0,0);" %)E..bamStatus.//1//(%%)
++DAQ channel: (% style="color: rgb(255,102,0);" %)FLASH.SDIAG/BAM/FL0.DBC2/ARRIVAL_TIME.BAMSTATUS(%%)
++desc: (% style="letter-spacing: 0.0px;" %) status bit: 0 - data is valid; 1 - beam present; 2 - calibration ongoing; 3 - feedback enabled; 4 - feedback acting;  mostly check for bit 0 == 1 is sufficient
++
++\\
++
++(% style="color: rgb(23,43,77);" %)SFELC(% style="color: rgb(255,102,0);" %)/electron bunch arrival time{{code language="none"}}/FL1/Electron Diagnostic/BAM/{{/code}}(%%)
++//always saved (PBD)//
++DOOCS prop : FLASH.SDIAG/BAM/(% style="color: rgb(23,43,77);" %)FL1.SFELC(%%)/ARRIVAL_TIME.absolute.SA1
++DAQ channel: (% style="color: rgb(255,102,0);" %)FLASH.SDIAG/BAM/(% style="color: rgb(255, 102, 0); color: rgb(23, 43, 77)" %)FL1.SFELC(% style="color: rgb(255,102,0);" %)/ARRIVAL_TIME.absolute.SA1 (%%)
++desc: Electron bunch arrival time measured  with the BAM  before the undulator (pulse resolved data). This one was newly installed in 2020.  The SA1 indicates the data is recorded for the first time slot at FLASh, typically used for FLASH1
++units: fs (bigger numbers (typically) indicate later arrival times of the electrons).
++
++\\
++
++(% style="color: rgb(23,43,77);" %)SFELC(% style="color: rgb(255,102,0);" %)/error{{code language="none"}}/FL1/Electron Diagnostic/BAM/{{/code}}(%%)
++//always saved (PBD)//
++DOOCS prop : FLASH.SDIAG/BAM/(% style="color: rgb(23,43,77);" %)FL1.SFELC(%%)/ARRIVAL_TIM(% style="color: rgb(0,0,0);" %)E.bamError(%%)
++DAQ channel: (% style="color: rgb(255,102,0);" %)FLASH.SDIAG/BAM/(% style="color: rgb(255, 102, 0); color: rgb(23, 43, 77)" %)FL1.SFELC(% style="color: rgb(255,102,0);" %)/ARRIVAL_TIME.BAMERROR(%%)
++desc: If the value is 0 , the BAM is working well. If it is non-zero there is a problem !!
++
++\\
++
++(% style="color: rgb(23,43,77);" %)SFELC(% style="color: rgb(255,102,0);" %)/error{{code language="none"}}/FL1/Electron Diagnostic/BAM/{{/code}}(%%)
++//always saved (PBD)//
++DOOCS prop : FLASH.SDIAG/BAM/(% style="color: rgb(23,43,77);" %)FL1.SFELC(%%)/ARRIVAL_TIM(% style="color: rgb(0,0,0);" %)E..bamStatus.//1//(%%)
++DAQ channel: (% style="color: rgb(255,102,0);" %)FLASH.SDIAG/BAM/(% style="color: rgb(255, 102, 0); color: rgb(23, 43, 77)" %)FL1.SFELC(% style="color: rgb(255,102,0);" %)/ARRIVAL_TIME.BAMSTATUS(%%)
++desc: (% style="" %) status bit: 0 - data is valid; 1 - beam present; 2 - calibration ongoing; 3 - feedback enabled; 4 - feedback acting;  mostly check for bit 0 == 1 is sufficient
++
++\\
++
  {{info title="BAM hints"}}
  * besides the arrivaltime from FLASH1 there is also the FLASH2/3 electron arrival time saved.In case of doubt ask your local contact
  * [[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]]
--* [[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"]]
++* [[LINK to detailed infos from MSK>>url:https://confluence.desy.de/display/SDiagPublic/BAM+Data+Structure||shape="rect"]]
  * a recent  [[talk about the working principle of the BAM>>attach:BAM-basics and outlook-2018_DESY-template_16-9Format.pdf]]
  {{/info}}
@@ -528,7 +528,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.DIAG/PBD.TOROID.ML/12EXP/CHARGE.TD{{/code}}
  DAQ channel: {{code language="none"}}TTF2.DIAG/PBD.TOROID.ML/12EXP{{/code}}
--desc: The bunch pattern as function of time in a burst recorded by toroide diagnostic BEHIND the undulator. (FLASH1)
++desc: The bunch pattern as function of time in a burst recorded by toroid diagnostic BEHIND the undulator. (FLASH1)
  units:
  \\
@@ -601,7 +601,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.FEL/TDOLFEL/TDOLFEL/STREAK.CAM.TIME{{/code}}
  DOOCS prop : {{code language="none"}}TTF2.FEL/TDOLFEL/TDOLFEL/STREAK.CAM.TIME{{/code}}
--desc: delaytime between the optical laser and the FEL units: ps
++desc: delay time between the optical laser and the FEL units: ps
  \\
@@ -611,7 +611,7 @@
  ==== User Data (FLASH1) ====
--The data saved specifically for detectors at an experiment will show up in /Experiment/ there is a large number of options for cameras or monitoring pslow properties (motor positons etc) for user experiments. For details please ask your local contact.
++The data saved specifically for detectors at an experiment will show up in /Experiment/ there is a large number of options for cameras or monitoring of slow properties (motor positions etc) for user experiments. For details please ask your local contact.
  NOTE: If parameters for an experiment are included on short notice the correct naming in the HDF5 may not be in time and the data will show up in /uncategorized/ with the DOOCS names
@@ -639,13 +639,13 @@
  {{code language="none"}}/FL1/Experiment/BL3/ADQ412 GHz ADC/CH03/TD{{/code}}
  DOOCS prop : {{code language="none"}}FLASH.FEL/ADC.ADQ.PG/EXP1.CH00/CH00.TD  or CH00.DAQ.TD{{/code}}
--here the {{code language="none"}}CH00.TD{{/code}} is the full ADC trace as it is sampled ( typically several 100.000 samples per pulse train) while the {{code language="none"}}CH00.DAQ.TD{{/code}} trace only has the number of samples which are sent to the DAQ OR if //grouping// is activated the {{code language="none"}}CH00.DAQ.TD{{/code}} conatins only the grouped spectra. To read the ADC trace with an online analysis program the {{code language="none"}}CH00.DAQ.TD{{/code}} is used preferablly.
++here the {{code language="none"}}CH00.TD{{/code}} is the full ADC trace as it is sampled ( typically several 100.000 samples per pulse train) while the {{code language="none"}}CH00.DAQ.TD{{/code}} trace only has the number of samples which are sent to the DAQ OR if //grouping// is activated the {{code language="none"}}CH00.DAQ.TD{{/code}} contains only the grouped spectra. To read the ADC trace with an online analysis program the {{code language="none"}}CH00.DAQ.TD{{/code}} is used preferably.
  DAQ channel: {{code language="none"}}FLASH.FEL/ADC.ADQ.PG/EXP1.CH00{{/code}}
  In addition there are also additional parameters saved like:
  * {{code language="none"}}sample frequency{{/code}}: it shows the sample frequency in MHz (number of samples per µs). NOTE: the clock of the ADC is NOT synchronized to the FLASH timing system. Thus the number of samples between bunches in the bunch train may be not integer numbers which will be show up for long bunch trains.
--* {{code language="none"}}number of samples{{/code}}: total number of samoles recorded for each 10 Hz trigger
++* {{code language="none"}}number of samples{{/code}}: total number of samples recorded for each 10 Hz trigger
  * {{code language="none"}}error (ADC):{{/code}} 0 indicates that there was no error
  ===== MHz ADCs =====
@@ -658,7 +658,7 @@
  In addition there are also additional parameters saved like:
  * {{code language="none"}}sample frequency{{/code}}: it shows the sample frequency in MHz (number of samples per µs). NOTE: the clock of the ADC is NOT synchronized to the FLASH timing system. Thus the number of samples between bunches in the bunch train may be not integer numbers which will be show up for long bunch trains.
--* {{code language="none"}}number of samples{{/code}}: total number of samoles recorded for each 10 Hz trigger
++* {{code language="none"}}number of samples{{/code}}: total number of samples recorded for each 10 Hz trigger
  [[Contents>>doc:||anchor="Contents"]]
@@ -819,7 +819,7 @@
  // saved opon request (PBD2)//
  DOOCS prop : {{code language="none"}}FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL040{{/code}}
  DAQ channel:{{code language="none"}} FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL040{{/code}}
--desc : meanwavelength ( ~~ 1 sec averaging time ) measured in the TUNNEL for a specific bunch out of the bunch train (via photoelectron spectroscopy)
++desc : mean wavelength ( ~~ 1 sec averaging time ) measured in the TUNNEL for a specific bunch out of the bunch train (via photoelectron spectroscopy)
  units : nm
  \\
@@ -833,11 +833,11 @@
  \\
--If Opis is running typically on the the averaged data is saved. For several experiments it may make sense to save the information for each single bunch. This is up to now done by savng the compleate ADC trace of the TOF setup. This is a huge amount of data and needs processing. This has to be performed after the beamtime in close contact to [[Markus Braune>>mailto:markus.braune@desy.de||shape="rect"]] ( respobsible for [[OPIS>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/opis_spectrometer/index_eng.html||shape="rect"]])
++If Opis is running typically on the the averaged data is saved. For several experiments it may make sense to save the information for each single bunch. This is up to now done by saving the complete ADC trace of the TOF setup. This is a huge amount of data and needs processing. This has to be performed after the beamtime in close contact to [[Markus Braune>>mailto:markus.braune@desy.de||shape="rect"]] ( responsible for [[OPIS>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/opis_spectrometer/index_eng.html||shape="rect"]])
  \\
--In case OPIS was not operating there is still informaton about the **set wavelength** for the undulators (see below) which may differ by up to 5 % from the actual wavelength due to different settings in the FEL ...
++In case OPIS was not operating there is still information about the **set wavelength** for the undulators (see below) which may differ by up to 5 % from the actual wavelength due to different settings in the FEL ...
  \\
@@ -856,8 +856,21 @@
  \\
--===== undulator settings =====
++===== electron bunch energy =====
++{{code language="none"}}/FL2/Electron Diagnostic/Electron energy/energy of first bunch/behind undulators{{/code}}
++//always saved (PBD2)//
++DOOCS prop : {{code language="none"}}FLASH.DIAG/BEAM_ENERGY_MEASUREMENT/FL2XTDS/ENERGY.FLASH2{{/code}}
++DAQ channel: (% style="color: rgb(94,108,132);" %)TTF2.DAQ/PBD2.BEAM.ENERGY.MEAS.ML.COPY/FL2XTDS.ENERGY.FLASH2{{code language="none"}}{{/code}}(%%)
++desc: electron bunch energy measured behind the undulator. Data is saved with 10 Hz - BUT (for computation reasons) only the energy of the FIRST bunch is recorded. The data is also available for (% style="color: rgb(94,108,132);" %)extraction and septum  in the beginning of FLASH2
++
++(% style="letter-spacing: 0.0px;" %)units: (% class="twikiNewLink" %)MeV
++
++\\
++
++(% style="color: rgb(94,108,132);font-weight: 600;letter-spacing: 0.0px;" %)
++undulator settings
++
  {{code language="none"}}/FL2/Electron Diagnostic/Undulator setting/set wavelength{{/code}}
  //always saved (PBD2)//
  DOOCS prop : {{code language="none"}}TTF2.FEEDBACK/FL2.WAVELENGTHCONTROL/FLASH2/WAVELENGTH{{/code}}

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