Changes for page The FLASH HDF5 structure

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

From 37.1 to 36.1 From 55.1 to 54.1

From version 54.1

edited by sndueste
on 2022/01/14 09:44

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To version 37.1

edited by cpassow
on 2020/11/23 16:26

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--XWiki.sndueste
++XWiki.cpassow

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@@ -1,6 +4,3 @@
--{{layout}}
--{{layout-section ac:type="single"}}
--{{layout-cell}}
  == Contents ==
@@ -19,38 +19,27 @@
  {{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 ==
++== The current FLASH HDF5 structure ==
--FLASH provides a conversion of its data acquisition (DAQ) to the commonly used [[HDF5>>url:https://www.hdfgroup.org/solutions/hdf5/||shape="rect"]] format. Correlated  data are mapped by a primary index called **train ID**. Every data set has an individual index of train IDs to identify the data even when data are missing or deviate in update rate. If the data set of choice contains gaps,  users have to decide how to treat missing values. DAQ channels are spread across various files with one file name pattern for each DAQ. This means users have to assemble data from different files if necessary.
++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 hierarchy is realized using a human readable named HDF tree with each DAQ channel containing the data sets "//value//" and "//index//". Additionally, the HDF group //zraw// contains a tree of the original DAQ channel names.
++* Electron Diagnostic
++* Photon Diagnostics
++* Beamlines
++* Experiment
++* Timing
++[[image:attach:HDF5_structure.jpg||height="400"]]
--Reference implementation, which follows the concept of Python libraries like Pandas, Xarray, or Dask, is given below.
++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"]]
--\\
++[[Contents>>doc:||anchor="Contents"]]
--{{expand title="Discontinued 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.
--
--All data sets were aligned by the same global index by filling in missing data. Fast DAQ channels  (pulse synchronous data - update 10 Hz) are filled in by NaN or 0, slow channels (not pulse synchronous data - update e.g. 1 Hz ) are interpolated by the DAQs libraries, by keeping the value constant up to the next change.
--
--While the near-online HDF files were converted live during the beamtime, the offline HDF files were manually compiled weeks/months later. Near-online HDF files were used by a provided API [[BeamtimeDaqAccess>>url:https://confluence.desy.de/display/FLASHUSER/Near-Online+data+analysis#Near-Onlinedataanalysis-BriefUserGuidetoBeamtimeDAQAccess||shape="rect"]], which also searches for DAQ channels in files. With assembled files "by run", all DAQ channels were existing in the same HDF file. While shorter runs usually fitted into one file, longer runs still had to be aggregated over several files. The creation of the assembled type of files still involves the use of fairly unstable DAQ Mex-functions As the environment required for using the Mex-functions is already deprecated, its continued existence is uncertain.
--
--The HDF hierarchy is almost identical in all formats. While in the the recent format each DAQ channel contains the data sets "value" and "index", the deprecated format had one data set for each DAQ channel. The deprecated formats supplies no time axis parameters for spectra data types.
--
  \\
--**HDF5 example files (old format)**
++=== HDF5 example files ===
  Here we have a few HDF5 samples (User data combined with Photon diagnostics data) from a few beamtimes showing the different kind options.
@@ -63,67 +63,26 @@
  \\
  \\
--{{/expand}}
--=== HDF examples: ===
--{{/layout-cell}}
--{{/layout-section}}
++[[Contents>>doc:||anchor="Contents"]]
--{{layout-section ac:type="three_equal"}}
--{{layout-cell}}
--*  ADC data as example for **fast** **data** (10 Hz):
--
  \\
--[[image:attach:image2020-11-16_15-26-28.png||height="250"]]
--{{/layout-cell}}
++== The new (starting 2021) HDF5 format ==
--{{layout-cell}}
--* The //average// FEL pulse energy as example for the **slow** **data** (different e.g. 1 Hz):
++Here is [[some documentation on the changes of the HDF5 format>>doc:FLASHUSER.HDF5 format]] that well be available in 2021 (work in progress)
--           ( every 10th train ID is listed in the HDF group "index")
--
  \\
--[[image:attach:image2020-11-16_15-31-45.png||height="250"]]
--{{/layout-cell}}
--
--{{layout-cell}}
--* (((
--//zraw// group contains the **original DAQ (DOOCS) names**
--)))
--
--           of the properties saved in the DESY internal raw format. (For experts)
--
  \\
--[[image:attach:image2020-11-16_16-26-3.png||height="400"]]
--{{/layout-cell}}
--{{/layout-section}}
--
--{{layout-section ac:type="single"}}
--{{layout-cell}}
--{{info}}
--=== Reference implementation (Python) ===
--
--(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" %)(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}}
--
--{{layout-section ac:type="single"}}
--{{layout-cell}}
--== Complete list of recordable parameters ==
--
--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"]].
--\\
--
  == 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:
++
  Note, the HDF group and data set names apply to our HDF tree version since vers. 0.3.0.
  \\
@@ -130,6 +130,8 @@
  === FLASH1 ===
++\\
++
  ==== Beamline info (FLASH1) ====
  {{code language="none"}}/FL1/Beamlines/Attenuator/pressure{{/code}}
@@ -204,15 +204,12 @@
  \\
--==== Photon Diagnostics SASE ([[GMD>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/gmd_intensity_and_position/index_eng.html||shape="rect"]]) ====
++==== Photon Diagnostics SASE ([[GMD>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/gmd_intensity_and_position/index_eng.html||shape="rect"]]) / Spectrometer (FLASH1) ====
--\\
--
--{{expand title="GMD format untill 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}}
--//always saved (PBD)//
++//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}}(%%)
@@ -222,6 +222,9 @@
  {{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}}
++
  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
@@ -237,6 +237,9 @@
  {{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}}
++
  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)
@@ -245,6 +245,8 @@
  {{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}}(%%)
  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
@@ -256,61 +256,9 @@
  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)**
--
--{{code language="none"}}/FL1/Photon Diagnostic/GMD/Average energy/energy tunnel{{/code}}
--//always saved (PBD)//
--(% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}} (%%)
--(% style="color: rgb(0,0,0);" %)DAQ channel: {{code language="none"}}FLASH.FEL/XGM.PHOTONFLUX/FL1.TUNNEL/PHOTONFLUX.UJ{{/code}}
--
--desc : calibrated average SASE Energy/pulse measured in the TUNNEL upstream the gas attenuator
--units : microJ
--
--\\
--
--{{code language="none"}}/FL1/Photon Diagnostic/GMD/Pulse resolved energy/energy tunnel{{/code}}
--//always saved (PBD)//
--
--(% style="color: rgb(0,0,0);" %)DOOCS prop :
--{{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL1.TUNNEL/INTENSITY.TD{{/code}}DAQ channel: {{code language="none"}}FLASH.FEL/XGM.INTENSITY/FL1.TUNNEL/INTENSITY.TD{{/code}}
--
--desc : Energy per pulse measured in the Tunnel.  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]]**
--
--{{info title="GMD pulse resolved data structure"}}
--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 information may be very noisy  - talk to your local contact)
--1. Position vertical  (mm, for a single pulse the position information 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
--
--
--[[image:attach:image2021-2-9_10-51-6.png||height="250"]]
--
--\\
--{{/info}}
--
--All values for the GMD are also available for the** BDA GMD **which is located in the experimental hall down stream the gas attenuator. If the attenuator is on the ratio between BDA and Tunnel signal shows the attenuation. **BUT NOTE** that the filter units  are downstream the GMD. So if filters  are used this influence is NOT measured by the GMD BDA !
--
--\\
--
--Besides  pulse energy the GMD also provides information about the beam position
--
  {{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}}
@@ -339,10 +339,6 @@
  desc :Beam position of the photon Beam determined by the GMD (TUNNEL, y=vertical)
  units : mm
--\\
--
--==== Spectrometer (FLASH1) ====
--
  {{code language="none"}}/FL1/Photon Diagnostic/Wavelength/Tunnelspectrometer/wavelength{{/code}}
  _always saved (when Spectrum is measured !!) (PBD) _
  DOOCS prop : {{code language="none"}}TTF2.EXP/PHOTONWL.ML/WAVE_LENGTH/VAL.TD{{/code}}
@@ -473,7 +473,7 @@
  ===== electron bunch energy =====
  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/average electron energy{{/code}}
--//always saved (PBD)//
++_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)
@@ -481,7 +481,7 @@
  \\
  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/pulse resolved energy{{/code}}
--//always saved (PBD)//
++_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
@@ -490,7 +490,7 @@
  \\
  {{code language="none"}}/FL1/Electron Diagnostic/Electron energy/wavelength bunch train average{{/code}}
--//always saved (PBD)//
++_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)
@@ -538,7 +538,7 @@
  //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 toroid diagnostic BEHIND the undulator. (FLASH1)
++desc: The bunch pattern as function of time in a burst recorded by toroide diagnostic BEHIND the undulator. (FLASH1)
  units:
  \\
@@ -611,7 +611,7 @@
  //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: delay time between the optical laser and the FEL units: ps
++desc: delaytime between the optical laser and the FEL units: ps
  \\
@@ -621,7 +621,7 @@
  ==== 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 of slow properties (motor positions 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 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
@@ -649,13 +649,13 @@
  {{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}} 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.
++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 samples recorded for each 10 Hz trigger
++* {{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 =====
@@ -668,7 +668,7 @@
  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 samples recorded for each 10 Hz trigger
++* {{code language="none"}}number of samples{{/code}}: total number of samoles recorded for each 10 Hz trigger
  [[Contents>>doc:||anchor="Contents"]]
@@ -684,12 +684,12 @@
  ==== Beamline info (FLASH2) ====
--{{code language="none"}}/FL2/Beamlines/Attenuator/pressure  {{/code}}
--(% style="color: rgb(0,0,0);" %)//always saved (PBD2)// (%%)
--(% style="color: rgb(0,0,0);" %)DOOCS prop : {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
--(% style="color: rgb(0,0,0);" %)DAQ channel:  {{code language="none"}}FLASH.FEL/ATT.GAS_DOSING/FL2.HALL/PRESSURE{{/code}} (%%)
--(% style="color: rgb(0,0,0);" %)desc: set pressure in the gas attenuator (%%)
--(% style="color: rgb(0,0,0);" %)units: mbar(%%)
++(% 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(%%)
  \\
  {{code language="none"}}/FL2/Beamlines/FL20/Shutter/open{{/code}}
@@ -708,13 +708,11 @@
  units: degree
  \\
--/FL2/Beamlines/Filter wheel/position wheel 2
--always saved (PBD2)
--DOOCS prop : {{code language="none"}}FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS{{/code}}
--DAQ channel: {{code language="none"}}FLASH.FEL/FL20H.PH.MOTOR/MOTOR2.MOT3/FPOS{{/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]]
--units: degree
++//always saved (PBD2)//
++\\\\**[[here>>doc:FLASHUSER.jddd-linked help pages.Filter-Units.Filter wheels in FLASH1 and FLASH2.WebHome]]**
++{{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}}
++
  \\
  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
@@ -736,37 +736,40 @@
  \\
++(% 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)
++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:FLASHUSER.jddd-linked help pages.Calibrating the pulse resolved (electron) data from GMD.WebHome]]**
--{{info title="GMD pulse resolved data structure"}}
--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 information may be very noisy  - talk to your local contact)
--1. Position vertical  (mm, for a single pulse the position information 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"]]
--\\
--{{/info}}
++{{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 !
  \\
@@ -793,15 +793,13 @@
  \\
--/FL2/Photon Diagnostic/GMD/Pulse resolved beam position/position tunnel x
--always saved (PBD2)
--DOOCS prop : FLASH.FEL/XGM.BPM/FL2.HALL/X.TD
--DAQ channel: FLASH.FEL/XGM.BPM/FL2.HALL:2
--desc: Besides the well calibrated averaged beam position information there is also the option 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
--(x=horizontal, y = vertial)
++//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}}
++{{code language="none"}}(x=horizontal, y = vertial){{/code}}
++
  again the same parameter set is available for the **HALL GMD**
  \\
@@ -829,7 +829,7 @@
  // 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 : mean wavelength ( ~~ 1 sec averaging time ) measured in the TUNNEL for a specific bunch out of the bunch train (via photoelectron spectroscopy)
++desc : meanwavelength ( ~~ 1 sec averaging time ) measured in the TUNNEL for a specific bunch out of the bunch train (via photoelectron spectroscopy)
  units : nm
  \\
@@ -843,11 +843,11 @@
  \\
--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 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"]])
++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"]])
  \\
--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 ...
++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 ...
  \\
@@ -866,21 +866,8 @@
  \\
--===== electron bunch energy =====
++===== undulator settings =====
--{{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}}
@@ -1210,6 +1210,68 @@
  [[Contents>>doc:||anchor="Contents"]]
  \\
--{{/layout-cell}}
--{{/layout-section}}
--{{/layout}}
++
++== Example code showing how to access HDF5 files ==
++
++\\
++
++=== Samples how to read HDF5 with Matlab ===
++
++The examples apply to HDF files with HDF tree version before vers. 0.3.0.
++
++(% style="color: rgb(0,128,0);" %)%% read in the needed data p=path; path(p,'D:\mess-daten\DAQ-data\hdf5\Gotthard') % add the actual folder to the path hdf5file='FLASH1_EXP-2016-03-16T1420.h5'; % data with Gotthard and VLS
++
++(% style="color: rgb(0,128,0);" %)% h5disp(hdf5file,'/','min') % to get an idea what is in the file % h5info(hdf5file,'/Experiment/Gotthard1/BL.0') % get info about the individual channel
++
++(% style="color: rgb(0,128,0);" %)% read a Number per 10 Hz pulse train:
++
++(% class="code" %)
++(((
++FEL_Wavelength_energy_server=h5read(hdf5file,'/Photon Diagnostic/Wavelength/Calculated by energy/wavelength' );
++)))
++
++(% style="color: rgb(0,128,0);" %)% read in a 1D array (spectrum) %GMD data GMD_Spectrum=h5read(hdf5file,'/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA');
++
++(% style="color: rgb(0,128,0);" %)% This reads in all the data . One can also limit the amount of data read to a subset of the data stored in the file. e.g. for image Data (Gotthard)
++
++\\
++
++(% class="code" %)
++(((
++Start_event= 500 ;   % define the first 10 Hz event
++ Number_of_events = 20; % how many 10 Hz events to load
++)))
++
++(% style="color: rgb(0,128,0);" %)% read only part of the data:
++
++(% class="code" %)
++(((
++Gotthard_data=h5read(hdf5file,'/Experiment/Gotthard1/BL.0',[2   650 Start_event],[50 85 Number_of_events]);
++)))
++
++(% style="color: rgb(0,128,0);" %)% start stop increment "manual" for 2 D data : [start bunch number in Gotthard data start pixelin spectrum start sample in 10 Hz trains], % [number of bunches in the Gotthard data number of points in the spectrum number of spectra ]
++
++(% class="code" %)
++(((
++VLS_Spectrum=h5read(hdf5file,'/Photon Diagnostic/Wavelength/VLS online spectrometer/PCO.ROI.X',[400 Start_event],[200 Number_of_events] );
++
++)))
++
++(% style="color: rgb(0,128,0);" %)% start stop increment "manual" for 1D data : [start sample in the spectrum start sample in 10 Hz trains],[number of points in the spectrum number of spectra ]
++
++(% style="color: rgb(0,128,0);" %)%GMD data
++
++(% class="code" %)
++(((
++GMD_Spectrum=h5read(hdf5file,'/Photon Diagnostic/GMD/Pulse resolved energy/energy BDA',[1 Start_event],[40 Number_of_events] );
++)))
++
++[[Contents>>doc:||anchor="Contents"]]
++
++\\
++
++== HDF5 and DOOCS ==
++
++Here is an outdated [[list with the available properties that are always saved (PBD) for FLASH1 as>>attach:FLASH1__DaqChannel2HdfNamePbd.xlsx]] HDF5 names and the corresponding DOOCS names
++
++[[Contents>>doc:||anchor="Contents"]]

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