Changes for page The FLASH HDF5 structure

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

From 10.1 to 11.1 From 18.1 to 19.1

From version 11.1

edited by sndueste
on 2019/09/17 16:50

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edited by sndueste
on 2019/09/18 10:09

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@@ -1,25 +1,8 @@
  == 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/}}
  \\
@@ -53,7 +53,7 @@
  \\
--== Most popular FLASH parameters and their names in HDF5 ==
++== Most popular FLASH parameters and their names in HDF5, DOOCS and (raw) DAQ ==
  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:
@@ -402,7 +402,7 @@
  //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 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 !)
++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 !)
  units:
  \\
@@ -409,7 +409,7 @@
  ===== Train time =====
  {{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
++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
  units: d h min s cs
  \\
@@ -475,9 +475,15 @@
  ==== 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:
@@ -500,14 +500,12 @@
  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:
--* sample frequency (in MHz)
--* error (state)
--* offset
++* {{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
--~|
--
  ===== MHz ADCs =====
  similar to the GHz ADCs the MHz ADCs are saved with HDF5 names like:
@@ -515,10 +515,19 @@
  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
@@ -526,11 +526,11 @@
  ==== Beamline info (FLASH2) ====
  (% style="color: rgb(255,153,0);" %)(not yet available){{code language="none"}}/FL2/Beamlines/Attenuator/pressure  {{/code}}(%%)
--//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
++(% 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(%%)
  \\
  {{code language="none"}}/FL2/Beamlines/FL20/Shutter/open{{/code}}
@@ -635,9 +635,7 @@
  \\
--\\
--
  //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}}
@@ -650,7 +650,7 @@
  \\
--==== 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"]]
@@ -689,18 +689,195 @@
  \\
++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)//
++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).
++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
++
++{{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 =====
++
++**FL1**{{code language="none"}}//Electron Diagnostic/BAM/4DBC3/electron bunch arrival time (low charge){{/code}}
++//always saved (PBD2)//
++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 (more or less) before the undulator (pulse resolved data)
++units: ps (bigger numbers indicate later arrivaltime of the electrons)
++
++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.
++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) ...
++
++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>>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"]]
++
++
++[[Contents>>doc:||anchor="Contents"]]
++
  \\
++==== Timing information, rep rate etc.  (FLASH2) ====
++
++===== 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
++
++===== 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)
++units: kHz
++
++===== 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)
++units:
  \\
++===== 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)
++units:
  \\
++===== Train ID =====
++
++{{code language="none"}}/Timing/train ID{{/code}}
++//always saved (PBD2)//
++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 !)
++units:
++\\
++
++===== Train time =====
++
++//always saved (PBD2)
++//{{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
++second column: microseconds
++third column: Train ID of FLASH
++\\
++
++[[Contents>>doc:||anchor="Contents"]]
++
++\\
++
++==== User Data (FLASH1) ====
++
++===== 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//
++\\The HDF5 names for the ADC traces are depending on the beamline :
++\\PG Beamline:
++{{code language="none"}}/FL1/Experiment/PG/ADQ412 GHz ADC/CH00/TD{{/code}}
++{{code language="none"}}/FL1/Experiment/PG/ADQ412 GHz ADC/CH01/TD{{/code}}
++{{code language="none"}}/FL1/Experiment/PG/ADQ412 GHz ADC/CH02/TD{{/code}}
++{{code language="none"}}/FL1/Experiment/PG/ADQ412 GHz ADC/CH03/TD{{/code}}
++
++BL Beamlines:
++{{code language="none"}}/FL1/Experiment/BL1/ADQ412 GHz ADC/CH00/TD{{/code}}
++{{code language="none"}}/FL1/Experiment/BL1/ADQ412 GHz ADC/CH01/TD{{/code}}
++{{code language="none"}}/FL1/Experiment/BL1/ADQ412 GHz ADC/CH02/TD{{/code}}
++{{code language="none"}}/FL1/Experiment/BL1/ADQ412 GHz ADC/CH03/TD{{/code}}
++\\{{code language="none"}}/FL1/Experiment/BL2/ADQ412 GHz ADC/CH00/TD{{/code}}
++{{code language="none"}}/FL1/Experiment/BL2/ADQ412 GHz ADC/CH01/TD{{/code}}
++\\{{code language="none"}}/FL1/Experiment/BL3/ADQ412 GHz ADC/CH02/TD{{/code}}
++{{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.
++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"}}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"}}/FL1/Experiment/BL1/SIS8300 100MHz ADC/CH2/TD{{/code}}
++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"]]
++
++\\
++
++\\
++
++\\
++
++\\
++
++\\
++
++\\
++
++\\
++
  (% class="wrapped" %)
  |=(((
  DAQ name

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