Changes for page The FLASH HDF5 structure

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

From 33.1 to 34.1 From 39.1 to 40.1

From version 34.1

edited by sndueste
on 2020/10/28 16:14

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To version 39.1

edited by sndueste
on 2021/02/09 11:53

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@@ -8,9 +8,9 @@
  == 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://www.hdfgroup.org/HDF5/||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://portal.hdfgroup.org/display/support||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"]]
++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"]]
  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"]]
--== FLASH HDF5 structure ==
++== The current 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 organised 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 organized according to train IDs. The general structure is:
  * Electron Diagnostic
  * Photon Diagnostics
@@ -27,16 +27,16 @@
  * Beamlines
  * Experiment
  * Timing
--[[~[~[image:url:http://hasfweb.desy.de/pub/Setup/HDF5main/HDF5_structure.jpg~|~|alt="HDF5_structure.jpg" width="700" height="500"~]~]>>attach:HDF5_structure.jpg]]
++[[image:attach:HDF5_structure.jpg||height="400"]]
--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]]
++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"]]
  \\
--== HDF5 example files ==
++=== 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.
@@ -54,8 +54,14 @@
  \\
++== 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"/}}
@@ -145,12 +145,14 @@
  \\
--==== 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) ====
++==== Photon Diagnostics SASE ([[GMD>>url:http://photon-science.desy.de/facilities/flash/photon_diagnostics/gmd_intensity_and_position/index_eng.html||shape="rect"]]) ====
++\\
++
++(% 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)//
--(% 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}}
++//always saved (PBD)//\\
  (% 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}}(%%)
@@ -160,9 +160,6 @@
  {{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
@@ -178,9 +178,6 @@
  {{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)
@@ -189,8 +189,6 @@
  {{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
@@ -205,6 +205,55 @@
  \\
++(% 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}}
@@ -233,6 +233,10 @@
  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}}
@@ -624,40 +624,37 @@
  \\
--(% 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 fromt of the gas attenuator and the apertures in the Hall)
++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]]**
--\\
++{{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
--{{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 )
++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"]]
--{{code language="none"}}{{/code}}
++\\
++{{/info}}
++\\
++
  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 !
  \\
@@ -1144,10 +1144,6 @@
  [[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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