Changes for page The FLASH HDF5 structure

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

From 12.1 to 11.1 From 39.1 to 38.1

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edited by sndueste
on 2021/02/09 10:51

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edited by sndueste
on 2019/09/17 16:57

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@@ -1,16 +1,33 @@
  == Contents ==
++\\
++* [[General information about HDF5>>doc:||anchor="General information about HDF5"]]
++* [[FLASH HDF5 structure>>doc:||anchor="FLASH HDF5 structure"]]
++* [[Most popular FLASH parameters and their names in HDF5>>doc:||anchor="Most popular FLASH parameters and their names in HDF5"]]
++** [[FLASH1>>doc:||anchor="FLASH1"]]
++*** [[Beamline info (FLASH1)>>doc:||anchor="Beamline info (FLASH1)"]]
++*** [[Photon Diagnostics SASE / Spectrometer (FLASH1)>>doc:||anchor="Photon Diagnostics SASE / Spectrometer (FLASH1)"]]
++*** [[Electron Beam properties (FLASH1)>>doc:||anchor="Electron Beam properties (FLASH1)"]]
++*** [[Timing information, rep rate etc.(FLASH1)>>doc:||anchor="Timing information, rep rate etc.(FLASH1)"]]
++*** [[Pump Probe Laser (FLASH1)>>doc:||anchor="Pump Probe Laser (FLASH1)"]]
++*** [[User Data (FLASH1)>>doc:||anchor="User Data (FLASH1)"]]
++** [[FLASH2>>doc:||anchor="FLASH2"]]
++** [[HDF5 structure revisions>>doc:||anchor="HDF5 structure revisions"]]
++* [[Example code showing how to access HDF5 files>>doc:||anchor="Example code showing how to access HDF5 files"]]
++** [[Samples how to read HDF5 with Matlab>>doc:||anchor="Samples how to read HDF5 with Matlab"]]
++** [[How to read HDF5 with Python via FLASHH5>>doc:||anchor="How to read HDF5 with Python via FLASHH5"]]
++* [[HDF5 and DOOCS>>doc:||anchor="HDF5 and DOOCS"]]
--{{toc/}}
++\\
  \\
  == General information about HDF5 ==
--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"]]
++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"]]
--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"]]
++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"]]
  For use on the DESY Maxwell or PAL (max-fsc or pal) **hdfview** is available in the xray module :
  {{code language="none"}}> module load xray{{/code}}
@@ -18,9 +18,9 @@
  [[Contents>>doc:||anchor="Contents"]]
--== The current FLASH HDF5 structure ==
++== FLASH HDF5 structure ==
--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:
++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:
  * Electron Diagnostic
  * Photon Diagnostics
@@ -27,45 +27,17 @@
  * Beamlines
  * Experiment
  * Timing
--[[image:attach:HDF5_structure.jpg||height="400"]]
++[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure.jpg~|~|alt="HDF5_structure.jpg" width="700" height="500"~]~]>>attach:HDF5_structure.jpg]]
--A detailed description of (most) channels can be found in the lower part of the hdf5 viewer:
--[[image:attach:HDF5_structure_desc.jpg||thumbnail="true" height="250"]]
++A detailled description of (most) channels can be found in the lower part of the hdf5 viewer:
++[[~[~[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]]
  [[Contents>>doc:||anchor="Contents"]]
  \\
--=== HDF5 example files ===
++== Most popular FLASH parameters and their names in HDF5 ==
--Here we have a few HDF5 samples (User data combined with Photon diagnostics data) from a few beamtimes showing the different kind options.
--
--[[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"]]
--
--\\
--
--[[~[~[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"]]
--
--\\
--
--\\
--
--[[Contents>>doc:||anchor="Contents"]]
--
--\\
--
--== The new (starting 2021) HDF5 format ==
--
--Here is [[some documentation on the changes of the HDF5 format>>doc:FLASHUSER.HDF5 format]] that well be available in 2021 (work in progress)
--
--\\
--
--\\
--
--== Most popular FLASH parameters and their names in HDF5, DOOCS and (raw) DAQ  ==
--
--{{id name="DOOCSparameters"/}}
--
  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"]].
  The most common and often used ones are summarized below:
@@ -107,7 +107,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.FEL/BLFILTERS1/FILTER1/FW.MOTOR.POS{{/code}}
  DAQ channel: {{code language="none"}}TTF2.FEL/BLFILTERS1/FILTER1/FW.MOTOR.POS{{/code}}
--desc: Position of the BL filter wheel 1 - to correlate with the filter material please look [[here>>doc:FLASHUSER.jddd-linked help pages.Filter-Units.Filter wheels in FLASH1 and FLASH2.WebHome]]
++desc: Position of the BL filter wheel 1 - to correlate with the filter material please look [[here>>doc:FLASH.Filter history (BL filterwheel 12)]]
  units: degree
  \\
@@ -115,7 +115,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.FEL/BLFILTERS2/FILTER2/FW.MOTOR.POS{{/code}}
  DAQ channel: {{code language="none"}}TTF2.FEL/BLFILTERS2/FILTER2/FW.MOTOR.POS{{/code}}
--desc: Position of the BL filter wheel 2 - to correlate with the filter material please look [[here>>doc:FLASHUSER.jddd-linked help pages.Filter-Units.Filter wheels in FLASH1 and FLASH2.WebHome]]
++desc: Position of the BL filter wheel 2 - to correlate with the filter material please look [[here>>doc:FLASH.Filter history (BL filterwheel 12)]]
  units: degree
  \\
@@ -145,7 +145,7 @@
  \\
--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
++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
  [[Contents>>doc:||anchor="Contents"]]
@@ -155,24 +155,17 @@
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
  //always saved (PBD)//
--(% style="color: rgb(165,173,186);" %)New MTCA Version: DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}} (%%)
--(% style="color: rgb(165,173,186);" %)New MTCA Version: DAQ channel: {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}}
--
--(% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT04/VAL{{/code}} (%%)
--(% style="color: rgb(0,0,0);" %)DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENPULSEIC{{/code}}(%%)
--desc : calibrated average SASE Energy/pulse measured in the TUNNEL upstream the gas attenuator (ion current)
++DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT04/VAL{{/code}}
++DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENPULSEIC{{/code}}
++desc : calibrated average SASE Energy/pulse measured in the TUNNEL before the attenuator (ion current)
  units : microJ
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
--//always saved (PBD)//
--
--(% style="color: rgb(193,199,208);" %)New MTCA Version: DOOCS prop :
--{{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}}
--
++//always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT34/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.USER{{/code}}
  desc :Energy per pulse Tunnel (from e-) - the values are set to "0" if there was no SASE beam in the FEL
--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]]**
++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]]
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel (raw){{/code}}
  //always saved (PBD)//
@@ -179,14 +179,10 @@
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT14/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.PHFLUX/TUNNEL.ENERGYPULSE.FF{{/code}}
  desc :Energy per pulse Tunnel (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]]**
++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]]
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy BDA{{/code}}
--//always saved (PBD)//
--
--(% style="color: rgb(165,173,186);" %)New MTCA Version: DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.BDA/PHOTONFLUX.UJ{{/code}} (%%)
--(% style="color: rgb(165,173,186);" %)New MTCA Version: DAQ channel: {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.BDA/PHOTONFLUX.UJ{{/code}}
--
++//always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT05/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENPULSEIC{{/code}}
  desc : calibrated average SASE Energy/pulse measured in the BDA (in the experimental hall) after the attenuator (ion current)
@@ -193,14 +193,11 @@
  units : microJ
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA{{/code}}
--//always saved (PBD)//
--
--(% style="color: rgb(193,199,208);" %)New MTCA Version: DOOCS prop :
--{{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}}(%%)
++//always saved (PBD)//
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT35/VAL{{/code}}
  DAQ channel: {{code language="none"}}PBD.PHFLUX/BDA.ENERGYPULSE.USER{{/code}}
  desc :Energy per pulse BDA (from e-) - the values are set to "0" if there was no SASE beam in the FEL
--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]]**
++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]]
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA (raw){{/code}}
  //always saved (PBD)//
@@ -207,15 +207,13 @@
  DOOCS prop : {{code language="none"}}TTF2.DAQ/PHFLUX/OUT15/VAL{{/code}}
  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]]**
++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]]
--\\
--
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA horizontal{{/code}}
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IX.POS{{/code}}
--desc :Beam position of the photon Beam determined by the GMD (BDA, x=horizontal)
++desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (BDA, x=horizontal)
  units : mm
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position BDA vertical{{/code}}
@@ -222,7 +222,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IY.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.BDA/IY.POS{{/code}}
--desc :Beam position of the photon Beam determined by the GMD (BDA, y=vertical)
++desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (BDA, y=vertical)
  units : mm
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position tunnel horizontal{{/code}}
@@ -229,7 +229,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IX.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IX.POS{{/code}}
--desc :Beam position of the photon Beam determined by the GMD (TUNNEL, x=horizontal)
++desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (TUNNEL, x=horizontal)
  units : mm
  {{code language="none"}}/FL1/Photon Diagnostic/GMD/Beam position/position tunnel vertical{{/code}}
@@ -236,7 +236,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IY.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL1.TUNNEL/IY.POS{{/code}}
--desc :Beam position of the photon Beam determined by the GMD (TUNNEL, y=vertical)
++desc :Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (TUNNEL, y=vertical)
  units : mm
  {{code language="none"}}/FL1/Photon Diagnostic/Wavelength/Tunnelspectrometer/wavelength{{/code}}
@@ -322,25 +322,10 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/4DBC3/LOW_CHARGE_ARRIVAL_TIME{{/code}}
  DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/4DBC3.LOW_CHARGE_ARRIVAL_TIME{{/code}}
--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)
++desc: Electron bunch arrival time measured with the BAM (more or less) before the undulator (pulse resolved data)
++units: ps (bigger numbers indicate later arrivaltime of the electrons)
++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>>url:https://confluence.desy.de/download/attachments/134216957/BAM-basics_and_outlook-2018_DESY-template_16-9Format.pdf?version=1&modificationDate=1565162143328&api=v2||shape="rect"]]
--{{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)
--
--{{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"]]
--* a recent  [[talk about the working principle of the BAM>>attach:BAM-basics and outlook-2018_DESY-template_16-9Format.pdf]]
--{{/info}}
--
--\\
--
  ===== electron beam profile =====
  {{code language="none"}}/FL1/Electron Diagnostic/Electron bunch profile/TDS profile{{/code}}
@@ -444,7 +444,7 @@
  //always saved (PBD)//
  DOOCS prop : {{code language="none"}}none{{/code}}
  DAQ channel: {{code language="none"}}none{{/code}}
--desc: Each 10 Hz burst has its unique train ID. For the HDF5 data set the ID is the same for all parameters with the same index (note camera images may be shifted by 1 ID - talk to the experts !)
++desc: Each 10 Hz burst has its unique train ID. For the HDF5 dataset the ID is the same for all parameters with the same index (note camera images may be shifted by 1 ID - talk to the experts !)
  units:
  \\
@@ -451,7 +451,7 @@
  ===== Train time =====
  {{code language="none"}}/Timing/train time{{/code}}
--desc:Local time as array of day, hour, minute, second, and centisecond. This data set is meant for visualization purposes only. For correlations use the train ID or the Unix time of the time stamp
++desc:Local time as array of day, hour, minute, second, and centisecond. This dataset is meant for visualisation purposes only. For correlations use the train ID or the Unix time of the time stamp
  units: d h min s cs
  \\
@@ -517,15 +517,9 @@
  ==== 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.
--
--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
--
--The most common and permanently installed device used by experiment are our ADCs:
--
  ===== GHz ADCs =====
--ADC traces of the (SPDevices 412) GHZ ADCs available for the users . More information about the ADCs can be found** [[here>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).MTCA ADCs.WebHome]]**
++ADC traces of the (SPDevices 412) GHZ ADCs available for the users . More information about the ADCs can be found [[here>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).MTCA ADCs.WebHome]]
  //saved on DEMAND in the user DAQ//
  \\The HDF5 names for the ADC traces are depending on the beamline :
  \\PG Beamline:
@@ -548,12 +548,14 @@
  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.
  DAQ channel: {{code language="none"}}FLASH.FEL/ADC.ADQ.PG/EXP1.CH00{{/code}}
--In addition there are also additional parameters saved like:
++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"}}error (ADC):{{/code}} 0 indicates that there was no error
++* sample frequency (in MHz)
++* error (state)
++* offset
++~|
++
  ===== MHz ADCs =====
  similar to the GHz ADCs the MHz ADCs are saved with HDF5 names like:
@@ -561,19 +561,10 @@
  DOOCS prop : FLASH.FEL/ADC.SIS.BL1/EXP1.CH02/CH00.TD
  DAQ channel: : FLASH.FEL/ADC.SIS.BL1/EXP1.CH02
--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
--
  [[Contents>>doc:||anchor="Contents"]]
--\\
--
--\\
--
--\\
--
  === FLASH2 ===
  There is analog to FLASH1 a permanently running "PhotonDagnostic DAQ FLASH2" (PBD2) and 2 User DAQs
@@ -581,11 +581,11 @@
  ==== Beamline info (FLASH2) ====
  (% style="color: rgb(255,153,0);" %)(not yet available){{code language="none"}}/FL2/Beamlines/Attenuator/pressure  {{/code}}(%%)
--(% style="color: rgb(193,199,208);" %)//always saved (PBD2)// (%%)
--(% style="color: rgb(193,199,208);" %)DOOCS prop : {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
--(% style="color: rgb(193,199,208);" %)DAQ channel:  {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
--(% style="color: rgb(193,199,208);" %)desc: set pressure in the gas attenuator (%%)
--(% style="color: rgb(193,199,208);" %)units: mbar(%%)
++//always saved (PBD2)//
++DOOCS prop : {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}}
++DAQ channel:  {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}}
++desc: set pressure in the gas attenuator
++units: mbar
  \\
  {{code language="none"}}/FL2/Beamlines/FL20/Shutter/open{{/code}}
@@ -600,13 +600,13 @@
  //always saved (PBD2)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/FL20H.PH.MOTOR/MOTOR1.MOT3/FPOS{{/code}}
  DAQ channel: FLASH.FEL/FL20H.PH.MOTOR/MOTOR1.MOT3/FPOS
--desc: Position of the BL filter wheel 1 - to correlate with the filter material please look **[[here>>doc:FLASHUSER.jddd-linked help pages.Filter-Units.Filter wheels in FLASH1 and FLASH2.WebHome]]**
++desc: Position of the BL filter wheel 1 - to correlate with the filter material please look [[here>>doc:FLASH.Filter history (BL filterwheel 12)]]
  units: degree
  \\
  //always saved (PBD2)//
--\\\\**[[here>>doc:FLASHUSER.jddd-linked help pages.Filter-Units.Filter wheels in FLASH1 and FLASH2.WebHome]]**
++\\\\[[here>>doc:FLASH.Filter history (BL filterwheel 12)]]
  {{code language="none"}}/FL2/Beamlines/Filter wheel/position wheel 2  DOOCS prop : FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS DAQ channel: FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS desc: Position of the BL filter wheel 2 - to correlate with the filter material please look units: degree{{/code}}
  \\
@@ -630,32 +630,38 @@
  \\
++(% style="color: rgb(255,204,0);" %)average Sigma    to be included in
++
++(% style="color: rgb(193,199,208);" %){{code language="none"}}/FL2/Photon Diagnostic/GMD/Average energy/energy tunnel uncertainty{{/code}} (%%)
++(% style="color: rgb(193,199,208);" %)//always saved (PBD2)// (%%)
++(% style="color: rgb(193,199,208);" %)DOOCS prop : FLASH.FEL/XGM.PHOTONFLUX/FL2.TUNNEL/PHOTONFLUX.UJ.SIGMA (%%)
++(% style="color: rgb(193,199,208);" %)DAQ channel: FLASH.FEL/XGM.PHOTONFLUX/FL2.TUNNEL/PHOTONFLUX.UJ.SIGMA (%%)
++(% style="color: rgb(193,199,208);" %)desc :  This parameter gives an indication of the error of the measurement of the average pulse energy. This takes signal to noise,  detector resolution, uncertainties in crossection etc into account. (it is NOT the measurement of the statistical fluctuation of the SASE pulses)(%%)
++(% style="color: rgb(193,199,208);" %)units : microJ
++
++\\
++
++\\
++
  {{code language="none"}}/FL2/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
  //always saved (PBD2)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL/INTENSITY.TD{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL/INTENSITY.TD{{/code}}
--desc : Energy per pulse measured in the Tunnel  (in front of the gas attenuator and the apertures in the Hall) In addition measurement errors and beam position are included for EACH pulse in the pulse train  !! (see below)
--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]]**
++desc : Energy per pulse measured in the Tunnel  (in fromt of the gas attenuator and the apertures in the Hall)
++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]]
--For every pulse in the pulse train the information is saved:
--
++\\
--1. **Intensity per pulse** (a.u. (more or less µJ ))
--1. Intensity per pulse (auxillary GMD) - not used
--1. Position horizontal (mm, for a single pulse the position informytion may be very noisy  - talk to your local contact)
--1. Position vertical  (mm, for a single pulse the position informytion may be very noisy  - talk to your local contact)
--1. **Intensity per pulse sigma**  (a.u. (more or less µJ ), (% style="color: rgb(0,0,0);" %)This parameter gives an indication of the error of the measurement of the pulse energy. This takes signal to noise,  detector resolution, uncertainties in crossection etc into account. (it is NOT the measurement of the statistical fluctuation of the SASE pulses)(%%))
--1. Position horizontal sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
--1. Position vertical sigma  (mm, indicates the error (RMS, sigma) of the measurement according to known uncertainties and signal to noise)
--1. Combined warning and error flags
++\\
--The pulse energy and the error are plotted for the first bunch of the pulse trains saved in this
--file
++{{code language="none"}}/FL2/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel uncertainty (sigma){{/code}}
++//always saved (PBD2)//
++DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL/INTENSITY.SIGMA.TD{{/code}}
++DAQ channel: {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL:4{{/code}}
++desc :(% style="color: rgb(0,0,0);" %)This parameter gives an indication of the error of the measurement of the pulse energy. This takes signal to noise,  detector resolution, uncertainties in crossection etc into account. (it is NOT the measurement of the statistical fluctuation of the SASE pulses)(%%)
++units : a.u. (more or less µJ - related to the value of the pulse energy )
--
--[[image:attach:image2021-2-9_10-51-6.png||height="250"]]
--
  {{code language="none"}}{{/code}}
  All values for the GMD are also available for the** HALL GMD **which is located in the experimental hall down stream the gas attenuator. If the attenuator is on the ratio between Hall and Tunnel signal shows the attenuation. **BUT NOTE** that the filter unit and the Aperture 4 are downstream the GMD. So if filters and aperture are used this influence is NOT measured by the GMD hall !
@@ -670,7 +670,7 @@
  //always saved (PBD2)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IX.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IX.POS{{/code}}
--desc : the Average ( ~~ 20 sec averaging time ) Beam position of the photon Beam determined by the GMD (tunnel, x=horizontal)
++desc : the Average ( ~~ 20 sec averaging time ) Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (tunnel, x=horizontal)
  units : mm
  \\
@@ -679,12 +679,14 @@
  //always saved (PBD2)//
  DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IY.POS{{/code}}
  DAQ channel: {{code language="none"}}FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IY.POS{{/code}}
--desc : the Average ( ~~ 20 sec averaging time ) Beam position of the photon Beam determined by the GMD (tunnel, x=horizontal)
++desc : the Average ( ~~ 20 sec averaging time ) Beam position of the photon Beam determined by the [[GMD>>doc:FLASH.Gas Monitor Detector]] (tunnel, x=horizontal)
  units : mm
  \\
++\\
++
  //always saved (PBD2)//
  \\\\{{code language="none"}}/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position tunnel x DOOCS prop : FLASH.FEL/XGM.BPM/FL2.HALL/X.TDDAQ channel: FLASH.FEL/XGM.BPM/FL2.HALL:2 desc: {{/code}}Besides the well calibrated averaged beam position information there is also the option
  {{code language="none"}}to measure the beam position on a single bunch level. HOWEVER this methide needs a perfectly adjusted signal level (talk to your local contact !!) and also then the signal to noise is rather small and one needs some averaging ... BUT with this option one can determine if there was a spatial slope on a burst (say forst bunches were lower than the last ones or so ...)units : mm    {{/code}}
@@ -697,9 +697,9 @@
  \\
--==== Photon Diagnostics OPIS[[  >>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/opis_spectrometer/index_eng.html||shape="rect"]](FLASH2) ====
++==== Photon Diagnostics OPIS[[ >>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/opis_spectrometer/index_eng.html||shape="rect"]](FLASH2) ====
--for more info see:** [[ OPIS>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/opis_spectrometer/index_eng.html||shape="rect"]]**
++for more info see: [[ OPIS>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/opis_spectrometer/index_eng.html||shape="rect"]]
  (The OPIS hall is not installed yet ...)
@@ -736,103 +736,116 @@
  \\
--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 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 ...
  \\
  \\
++\\
++
  ==== Electron Beam properties (FLASH2) ====
  ===== bunch charge =====
  {{code language="none"}}/FL2/Electron Diagnostic/Bunch charge/after undulator{{/code}}
--//always saved (PBD2)//
++//always saved (PBD)//
  DOOCS prop : {{code language="none"}}FLASH.DIAG/PBD2.TOROID.ML/9FL2BURN/CHARGE.FLASH2{{/code}}
  DAQ channel: {{code language="none"}}FLASH.DIAG/PBD2.TOROID.ML/9FL2BURN/CHARGE.FLASH2{{/code}}
--desc: electron bunch charge FLASH2 (average value for each bunchtrain).
++desc: electron bunch charge (FLASH2)
  units: nC
  \\
--===== 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}}
--DAQ channel:  {{code language="none"}}TTF2.FEEDBACK/FL2.WAVELENGTHCONTROL/FLASH2/WAVELENGTH{{/code}}
--desc: Set value for the anticipated wavelength . This parameter is used to set the undulator gap. It may however deviate from the actual wavelength by several % ...
--units: nm
++|(((
++FLASH.UTIL/FL2.UND.MOTOR/FL2SASE14/GAP
++)))|(((
++/FL2/Electron Diagnostic/Undulator setting/SASE14 gap
++)))
++|(((
++TTF2.FEEDBACK/FL2.WAVELENGTHCONTROL/FLASH2/WAVELENGTH
++)))|(((
++/FL2/Electron Diagnostic/Undulator setting/set wavelength
++)))
--{{code language="none"}}/FL2/Electron Diagnostic/Undulator setting/SASE14 gap{{/code}}
--//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.UTIL/FL2.UND.MOTOR/FL2SASE14/GAP{{/code}}
--DAQ channel:  {{code language="none"}}FLASH.UTIL/FL2.UND.MOTOR/FL2SASE14/GAP{{/code}}
--desc: gap value of the undulators. This can be used to follow up how many undulators were closed and if there was a taper
--units: mm
--
--The gap values are saved for all 12 undulators (Nr 3 to 14). Undulator 14 is the one closest to the experimental hall.
--
  =====
  arrival time =====
--{{code language="none"}}/FL2/Electron Diagnostic/BAM/8FL2XTDS/electron bunch arrival time (low charge){{/code}}
--//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.SDIAG/BAM/8FL2XTDS/LOW_CHARGE_ARRIVAL_TIME{{/code}}
--DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/8FL2XTDS.LOW_CHARGE_ARRIVAL_TIME{{/code}}
--desc: Electron bunch arrival time measured with the BAM after the FLASH2 undulator (pulse resolved data)
--units: ps (bigger numbers indicate later arrivaltime of the electrons)
--
--**FL1**{{code language="none"}}//Electron Diagnostic/BAM/4DBC3/electron bunch arrival time (low charge){{/code}}
--//always saved (PBD2)//
++{{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}}
  DAQ channel: {{code language="none"}}FLASH.SDIAG/BAM.DAQ/4DBC3.LOW_CHARGE_ARRIVAL_TIME{{/code}}
--desc: Electron bunch arrival time measured with the BAM  in the accelerator  (pulse resolved data)
--units: ps (bigger numbers indicate later arrivaltime of the electrons)
++desc: Electron bunch arrival time measured with the BAM (more or less) before the undulator (pulse resolved data)
++units: ps (bigger numbers indicate later arrivaltime of the electrons)
++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>>url:https://confluence.desy.de/download/attachments/134216957/BAM-basics_and_outlook-2018_DESY-template_16-9Format.pdf?version=1&modificationDate=1565162143328&api=v2||shape="rect"]]
  \\
--{{info title="BAM hints"}}
--* The BAM 4DBC3 measures the arrivaltime of** FLASH 1 and FLASH2** in the same data set (thus also sorted in at /FL1/ !).
--* 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
--** 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
--* [[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"]]
--* a recent  [[talk about the working principle of the BAM>>attach:BAM-basics and outlook-2018_DESY-template_16-9Format.pdf]]
--{{/info}}
++\\
++\\
--[[Contents>>doc:||anchor="Contents"]]
++===== electron bunch energy =====
++{{code language="none"}}/FL1/Electron Diagnostic/Electron energy/average electron energy{{/code}}
++_always saved (PBD)
++DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/E_INTRA_MEAN/VAL{{/code}}
++DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/E_MEAN{{/code}}
++desc: electron bunch energy (average over the bunch train)
++units: (% class="twikiNewLink" %)MeV(%%)
  \\
--==== Timing information, rep rate etc.  (FLASH2) ====
++{{code language="none"}}/FL1/Electron Diagnostic/Electron energy/pulse resolved energy{{/code}}
++_always saved (PBD)
++DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/E_SPECT/VAL.TD{{/code}}
++DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/E_SPECT{{/code}}
++desc: electron bunch energy bunch resolved
++units: (% class="twikiNewLink" %)MeV
--===== start time of FLASH2 =====
++\\
--{{code language="none"}}/FL2/Timing/start time flash2{{/code}}
--//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.DIAG/TIMER/FLASHCPUTIME1.0/BUNCH_POSITION.2{{/code}}
--DAQ channel: {{code language="none"}}FLASH.DIAG/TIMER/FLASHCPUTIME1.0/BUNCH_POSITION.2{{/code}}
--desc: The max 600 µs acceleration time of FLASH is devided between FLASH1 and FLASH2. This 600 µs window starts with FLASH1 (up to now)  at a time"label" of 700 µs (for historic reasons). Thus the first bunch of FLASH 1 comes at "700" and the last possibel bunch comes at 1300 (700+600). After FLASH1 train is over ther is a about 70µs switching time with no bunches. Then comes the first FLASH2 bunch.  Thus if e.g. the start time of FLASH2 is 1200 it means that FLASH2 starts at column 500 (1200-700)  in the HDF5 files. (However for yet unknown reasons this may change by 2-3 colums ...)
--units: µs
++{{code language="none"}}/FL1/Electron Diagnostic/Electron energy/wavelength bunch train average{{/code}}
++_always saved (PBD)
++DOOCS prop : {{code language="none"}}TTF2.DAQ/ENERGY.DOGLEG/LAMBDA_MEAN/VAL{{/code}}
++DAQ channel: {{code language="none"}}PBD.ENERGY.DOGLEG/LAMBDA_MEAN{{/code}}
++desc: Wavelength calculated by the electron bunch energy (average over the bunch train) (FLASH1)
++units: nm
++\\
++[[Contents>>doc:||anchor="Contents"]]
++
++\\
++
++==== Timing information, rep rate etc.  (FLASH1) ====
++
  ===== bunch repetition rate =====
--{{code language="none"}}/FL2/Timing/repetition rate{{/code}}
--//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.DIAG/TIMER/FLASHCPUTIME1.0/REP_RATE_KHZ.2{{/code}}
--DAQ channel: {{code language="none"}}FLASH.DIAG/TIMER/FLASHCPUTIME1.0/REP_RATE_KHZ.2{{/code}}
--desc: repetition rate of the bunches / pulses within the burst (FLASH2)
++{{code language="none"}}/FL1/Timing/repetition rate{{/code}}
++//always saved (PBD)//
++DOOCS prop : {{code language="none"}}FLASH.DIAG/TIMER/FLASHCPUTIME1.0/REP_RATE_KHZ.1{{/code}}
++DAQ channel: {{code language="none"}}TTF2.UTIL/LASER.CONTROL/GUN/PULSE_FREQ{{/code}}
++desc: repetition rate of the bunches / pulses within the burst (FLASH1)
  units: kHz
++\\
++===== set number of pulses =====
++
++{{code language="none"}}/FL1/Timing/set number of bunches{{/code}}
++//always saved (PBD)//
++DOOCS prop : {{code language="none"}}FLASH.DIAG/TOROID.ML/3GUN/NUMBEROFBUNCHES.FLASH1{{/code}}
++DAQ channel: {{code language="none"}}TTF2.UTIL/LASER.CONTROL/GUN/PULSE_NUM{{/code}}
++desc: Number of pulses set at the gun (FLASH1)
++units:
++
  ===== actual number of pulses =====
  {{code language="none"}}/FL1/Timing/actual number of bunches{{/code}}
--//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.DIAG/PBD2.TOROID.ML/3GUN/NUMBEROFBUNCHES.FLASH2{{/code}}
--DAQ channel: {{code language="none"}}FLASH.DIAG/PBD2.TOROID.ML/3GUN/NUMBEROFBUNCHES.FLASH2{{/code}}
--desc: Number of bunches measured BEHIND the undulator. If pulses are used for diagnostic of the protection system of the accelerator limits the number of bunches to be accelerated this is the actual number that created XUV radiation.The number is calculated by the DAQ middle layer server, (FLASH2)
++//always saved (PBD)//
++DOOCS prop : {{code language="none"}}FLASH.DIAG/TOROID.ML/12EXP/NUMBEROFBUNCHES.FLASH1{{/code}}
++DAQ channel: {{code language="none"}}TTF2.DIAG/PBD.TOROID.ML/12EXP{{/code}}
++desc: Number of bunches measured BEHIND the undulator. If pulses are used for diagnostic of the protection system of the accelerator limits the number of bunches to be accelerated this is the actual number that created XUV radiation.The number is calculated by the DAQ middle layer server, (FLASH1)
  units:
  \\
@@ -839,10 +839,10 @@
  ===== actual pulse pattern recorded after the undulator =====
  {{code language="none"}}/FL1/Timing/Bunch pattern/pattern after undulator{{/code}}
--//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.DIAG/PBD2.TOROID.ML/9FL2BURN.PULSEPATTERN{{/code}}
--DAQ channel: {{code language="none"}}FLASH.DIAG/PBD2.TOROID.ML/9FL2BURN.PULSEPATTERN{{/code}}
--desc: The bunch pattern as function of time in a burst recorded by toroide diagnostic BEHIND the undulator. (FLASH2)
++//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)
  units:
  \\
@@ -849,7 +849,7 @@
  ===== Train ID =====
  {{code language="none"}}/Timing/train ID{{/code}}
--//always saved (PBD2)//
++//always saved (PBD)//
  DOOCS prop : {{code language="none"}}none{{/code}}
  DAQ channel: {{code language="none"}}none{{/code}}
  desc: Each 10 Hz burst has its unique train ID. For the HDF5 dataset the ID is the same for all parameters with the same index (note camera images may be shifted by 1 ID - talk to the experts !)
@@ -858,16 +858,13 @@
  ===== Train time =====
--//always saved (PBD2)
--//{{code language="none"}}/Timing/train time{{/code}}
++{{code language="none"}}/Timing/train time{{/code}}
  desc:Local time as array of day, hour, minute, second, and centisecond. This dataset is meant for visualisation purposes only. For correlations use the train ID or the Unix time of the time stamp
  units: d h min s cs
  \\
--{{code language="none"}}/Timing/time stamp{{/code}}
--
--//always saved (PBD2)//
--desc: first column: Local time in unix time. To get day, hour, minute, second you can use unix: e.g. date ~-~-date='@1553617729' or matlab, python etc
++{{code language="none"}}/Timing/time stamp{{/code}}
++desc:first column: Local time in unix time. To get day, hour, minute, second you can use unix: e.g. date ~-~-date='@1553617729' or matlab, python etc
  second column: microseconds
  third column: Train ID of FLASH
  \\
@@ -876,102 +876,209 @@
  \\
--==== User Data (FLASH2) ====
++\\
--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.
--
--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
--
--The most common and permanently installed device used by experiment are our ADCs:
--
--===== GHz ADCs =====
--
--ADC traces of the (SPDevices 412) GHZ ADCs available for the users . More information about the ADCs can be found** [[here>>doc:FLASHUSER.Data Acquisition and controls.Controls (DOOCS, jDDD,\.\.\.).MTCA ADCs.WebHome]]**
--//saved on DEMAND in the user DAQ//
--\\Up to now there are 4 channels available at FL24
--\\\\{{code language="none"}}/FL2/Experiment/MTCA-EXP1/ADQ412 GHz ADC/CH00/TD{{/code}}
--{{code language="none"}}/FL2/Experiment/MTCA-EXP1/ADQ412 GHz ADC/CH01/TD{{/code}}
--\\{{code language="none"}}/FL2/Experiment/MTCA-EXP1/ADQ412 GHz ADC/CH02/TD{{/code}}{{code language="none"}}/FL2/Experiment/MTCA-EXP1/ADQ412 GHz ADC/CH03/TD{{/code}}
--
  \\
--DOOCS prop : {{code language="none"}}FLASH.FEL/ADC.ADQ.FL2EXP1/FL2EXP1.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.
--DAQ channel: {{code language="none"}}FLASH.FEL/ADC.ADQ.FL2EXP1/FL2EXP1.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"}}error (ADC):{{/code}} 0 indicates that there was no error
--* {{code language="none"}}/CH0-CH3/offset{{/code}}: To use the full dynamic range of the ADC one can shift the base line . This offset is saved here.
--
--===== MHz ADCs =====
--
--similar to the GHz ADCs the MHz ADCs are saved with HDF5 names like:
--{{code language="none"}}/FL2/Experiment/MTCA-EXP1/SIS8300 100MHz ADC/CH2/TD{{/code}}
--DOOCS prop : FLASH.FEL/ADC.SIS.FL2EXP1/FL2EXP1.CH02/CH00.TD
--DAQ channel: : FLASH.FEL/ADC.SIS.FL2EXP1/FL2EXP1.CH02
--
--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
--
--[[Contents>>doc:||anchor="Contents"]]
--
  \\
  \\
--==== Pump Probe Laser (FLASH2) ====
--
--There may be more information available from the "Laser DAQ". laese contact your Laser Local Contact.
--
--
--{{code language="none"}}/FL2/Experiment/Pump probe laser/FL24/attenuator position{{/code}}//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.FEL/FLAPP2BEAMLINES/MOTOR1.FL24/FPOS{{/code}}
--DAQ channel: {{code language="none"}}FLASH.FEL/FLAPP2BEAMLINES/MOTOR1.FL24/FPOS{{/code}}
--desc: attenuation of the PPLaser in the FL24 hutch (rotation of a waveplate)
--units : deg.
--
  \\
--
--{{code language="none"}}/FL2/Experiment/Pump probe laser/FL24/polarization position{{/code}}//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.FEL/FLAPP2BEAMLINES/MOTOR2.FL24/FPOS{{/code}}
--DAQ channel: {{code language="none"}}FLASH.FEL/FLAPP2BEAMLINES/MOTOR2.FL24/FPOS{{/code}}
--desc: attenuation of the PPLaser in the FL24 hutch (rotation of a waveplate)
--units : deg.
--
  \\
--{{code language="none"}}/FL1/Experiment/Pump probe laser/laser delay readback{{/code}}
--//always saved (PBD2)//
--DOOCS prop : {{code language="none"}}FLASH.SYNC/LASER.LOCK.EXP/FLASH2.PPL1.OSC1/FMC0.MD22.0.POSITION.RD{{/code}}
--DAQ channel: {{code language="none"}}FLASH.SYNC/LASER.LOCK.EXP/FLASH2.PPL1.OSC1/FMC0.MD22.0.POSITION.RD{{/code}}
--desc: delay of the Pump probe laser - measured by the read back position of the motor. There is also the set value available ( upto now these values are only updating every 1-2 seconds. There is no fast encoder property as on FLASH1 available)
--units : ps )
++(% class="wrapped" %)
++|=(((
++DAQ name
++)))|=(((
++HDF5 name
++)))
++|(((
++FLASH.UTIL/FL2.UND.MOTOR/FL2SASE3/GAP
++)))|(((
++/FL2/Electron Diagnostic/Undulator setting/SASE03 gap
++)))
++|(((
++FLASH.UTIL/FL2.UND.MOTOR/FL2SASE14/GAP
++)))|(((
++/FL2/Electron Diagnostic/Undulator setting/SASE14 gap
++)))
++|(((
++TTF2.FEEDBACK/FL2.WAVELENGTHCONTROL/FLASH2/WAVELENGTH
++)))|(((
++/FL2/Electron Diagnostic/Undulator setting/set wavelength
++)))
++|(((
++FLASH.FEL/XGM.PHOTONFLUX/FL2.HALL/PHOTONFLUX.UJ
++)))|(((
++/FL2/Photon Diagnostic/GMD/Average energy/hall
++)))
++|(((
++FLASH.FEL/XGM.PHOTONFLUX/FL2.HALL/PHOTONFLUX
++)))|(((
++/FL2/Photon Diagnostic/GMD/Average energy/hall (raw)
++)))
++|(((
++FLASH.FEL/XGM.PHOTONFLUX/FL2.TUNNEL/PHOTONFLUX.UJ
++)))|(((
++/FL2/Photon Diagnostic/GMD/Average energy/tunnel
++)))
++|(((
++FLASH.FEL/XGM.PHOTONFLUX/FL2.TUNNEL/PHOTONFLUX
++)))|(((
++/FL2/Photon Diagnostic/GMD/Average energy/tunnel (raw)
++)))
++|(((
++FLASH.FEL/XGM.POSMON/FL2.HALL/IX.POS
++)))|(((
++/FL2/Photon Diagnostic/GMD/Average beam position/position hall horizontal
++)))
++|(((
++FLASH.FEL/XGM.POSMON/FL2.HALL/IY.POS
++)))|(((
++/FL2/Photon Diagnostic/GMD/Average beam position/position hall vertical
++)))
++|(((
++FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IX.POS
++)))|(((
++/FL2/Photon Diagnostic/GMD/Average beam position/position tunnel horizontal
++)))
++|(((
++FLASH.FEL/XGM.POSMON/FL2.TUNNEL/IY.POS
++)))|(((
++/FL2/Photon Diagnostic/GMD/Average beam position/position tunnel vertical
++)))
++|(((
++FLASH.FEL/XGM.BPM/FL2.HALL:0
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position hall horizontal
++)))
++|(((
++FLASH.FEL/XGM.BPM/FL2.HALL:1
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position hall vertical
++)))
++|(((
++FLASH.FEL/XGM.BPM/FL2.TUNNEL:0
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position tunnel horizontal
++)))
++|(((
++FLASH.FEL/XGM.BPM/FL2.TUNNEL:1
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position tunnel vertical
++)))
++|(((
++FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL:1
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved energy/energy aux tunnel
++)))
++|(((
++FLASH.FEL/XGM.INTENSITY/FL2.HALL
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved energy/energy hall
++)))
++|(((
++FLASH.FEL/XGM.INTENSITY/FL2.HALL:0
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved energy/energy hall
++)))
++|(((
++FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel
++)))
++|(((
++FLASH.FEL/XGM.INTENSITY/FL2.TUNNEL:0
++)))|(((
++/FL2/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel
++)))
++|(((
++FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL042
++)))|(((
++/FL2/Photon Diagnostic/Wavelength/OPIS tunnel/Processed/mean phtoton energy
++)))
++|(((
++FLASH.UTIL/STORE/FL2.TUNNEL.OPIS/VAL040
++)))|(((
++/FL2/Photon Diagnostic/Wavelength/OPIS tunnel/Processed/mean wavelengt
++)))
++|(((
++FLASH.FEL/ADC.ADQ/OPIS1.CH02
++)))|(((
++/FL2/Photon Diagnostic/Wavelength/OPIS tunnel/Raw data/CH02
++)))
++|(((
++FLASH.DIAG/PBD2.TOROID.ML/9FL2BURN/CHARGE.FLASH2
++)))|(((
++/FL2/Electron Diagnostic/Bunch charge/after undulator
++)))
++|(((
++FLASH.DIAG/PBD2.TOROID.ML/3GUN/CHARGE.FLASH2
++)))|(((
++/FL2/Electron Diagnostic/Bunch charge/at gun
++)))
++|(((
++FLASH.FEL/FL20T.PH.MOTOR/MOTOR1.MOT1/FPOS
++)))|(((
++/FL2/Beamlines/Tunnel Apertures/position aperture1 horizontal
++)))
++|(((
++FLASH.FEL/FL20T.PH.MOTOR/MOTOR2.MOT1/FPOS
++)))|(((
++/FL2/Beamlines/Tunnel Apertures/position aperture1 vertical
++)))
++|(((
++FLASH.FEL/ADC.SIS.FL2FS/FL20.SHUTTER
++)))|(((
++/FL2/Beamlines/FL20/Shutter/channel 0
++)))
++|(((
++FLASH.FEL/ADC.ADQ.FL2EXP1/FL2EXP1.CH00
++)))|(((
++/FL2/Experiment/MTCA-EXP1/ADQ412 GHz ADC/CH00/TD
++)))
++|(((
++FLASH.FEL/ADC.SIS.FL2EXP1/FL2EXP1.CH00
++)))|(((
++/FL2/Experiment/MTCA-EXP1/SIS8300 100MHz ADC/CH0/TD
++)))
++|(((
++FLASH.SYNC/LASER.LOCK.EXP/FLASH2.PPL1.OSC1/CURRENT_INPUT_JITTER.RD
++)))|(((
++/FL2/Experiment/Pump probe laser/Synchronization/timing jitter RMS
++)))
++|(((
++FLASH.SYNC/LASER.LOCK.EXP/FLASH2.PPL1.OSC1/LOCK_STATUS.VALUE.RD
++)))|(((
++/FL2/Experiment/Pump probe laser/Synchronization/timing jitter RMS GECCO
++)))
++|(((
++FLASH.SYNC/LASER.LOCK.EXP/FLASH2.PPL1.OSC1/FMC0.MD22.0.POSITION.RD
++)))|(((
++/FL2/Experiment/Pump probe laser/laser delay readback
++)))
++|(((
++FLASH.SYNC/LASER.LOCK.EXP/FLASH2.PPL1.OSC1/FMC0.MD22.0.POSITION_SET.WR
++)))|(((
++/FL2/Experiment/Pump probe laser/laser delay set value
++)))
++|(((
++FLASH.FEL/FLAPP2BEAMLINES/MOTOR1.FL24/FPOS
++)))|(((
++/FL2/Experiment/Pump probe laser/FL24/attenuator position
++)))
++|(((
++FLASH.FEL/FLAPP2BEAMLINES/MOTOR2.FL24/POS
++)))|(((
++/FL2/Experiment/Pump probe laser/FL24/polarization position
++)))
  \\
--{{code language="none"}}/FL1/Experiment/Pump probe laser/Synchronization/timing jitter RMS{{/code}}
--//always saved (PBD)//
--DOOCS prop : {{code language="none"}}FLASH.SYNC/LASER.LOCK.EXP/FLASH2.PPL1.OSC1/CURRENT_INPUT_JITTER.RD{{/code}}
--DAQ channel: {{code language="none"}}FLASH.SYNC/LASER.LOCK.EXP/FLASH2.PPL1.OSC1/CURRENT_INPUT_JITTER.RD{{/code}}
--desc: rms jitter of the fs-Oscillator
--units: fs
--
  [[Contents>>doc:||anchor="Contents"]]
--\\
--
--=== "/uncategorized/" ===
--
-- 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 their DOOCS names
--
--\\
--
  === HDF5 structure revisions ===
  Starting with Beamblock 4, August 2018, the hierarchy of the HDF group names have been adapted to reflect the new situation at FLASH. FLASH2 is operating for users quite some time now. Therefore, both accelerators appear equally in their respective HDF groups, namely "/FL1" and "/FL2". The root group of proper, by run organised HDF files have an attribute called "version". This version attribute has changed from "0.2.x" to "0.3.x". The changes in detail:
@@ -1144,6 +1144,10 @@
  [[Contents>>doc:||anchor="Contents"]]
++=== How to read HDF5 with Python via FLASHH5 ===
++
++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.
++
  \\
  == HDF5 and DOOCS ==

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