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Last modified by makuadm on 2026-01-07 06:21
From version 46.1
edited by makuadm
on 2026-01-06 23:43
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_23.WebHome] has been updated!
To version 41.2
edited by sndueste
on 2025-02-05 11:21
Change comment: Update document after refactoring.

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1 -FLASHUSER.Offline data analysis (DAQ).WebHome
1 +FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).WebHome
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1 -XWiki.makuadm
1 +XWiki.sndueste
Content
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1 -Experimental data is recorded as HDF files[[~[link~]>>doc:FS-FLASH USER tmp.Data Acquisition and controls 1.DAQ and controls overview.Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]] on the GPFS file system[[~[link~]>>https://docs.desy.de/asap3/]]. The access rights are linked to the user's DESY account and can be managed by the PI via the GAMMA portal[[~[link~]>>url:https://gamma-portal.desy.de/||shape="rect"]]. The experimental data can be downloaded via the GAMMA portal, but it is advised to use the DESY computing infrastructure. Access point are via ssh, Maxwell-Display Server[[~[link~]>>url:https://confluence.desy.de/display/MXW/Maxwell+Cluster||shape="rect"]] or JuyterHub[[~[link~]>>url:https://confluence.desy.de/display/MXW/JupyterHub+on+Maxwell||shape="rect"]]. We recommend using the JupyterHub for data exploration and the SLURM resources for high performances computing - see FAB for easy usage of the infrastructure.
1 +Experimental data is recorded as HDF files[[~[link~]>>doc:FLASHUSER.Data Acquisition and controls.Data Access at FLASH (DAQ, gpfs,\.\.\.).Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]] on the GPFS file system[[~[link~]>>doc:ASAP3.ASAP3 Data Storage for PETRA III]]. The access rights are linked to the user's DESY account and can be managed by the PI via the GAMMA portal[[~[link~]>>url:https://gamma-portal.desy.de/||shape="rect"]]. The experimental data can be downloaded via the GAMMA portal, but it is advised to use the DESY computing infrastructure. Access point are via ssh, Maxwell-Display Server[[~[link~]>>url:https://confluence.desy.de/display/MXW/Maxwell+Cluster||shape="rect"]] or JuyterHub[[~[link~]>>url:https://confluence.desy.de/display/MXW/JupyterHub+on+Maxwell||shape="rect"]]. We recommend using the JupyterHub for data exploration and the SLURM resources for high performances computing - see FAB for easy usage of the infrastructure.
2 2  
3 3  {{info title="How to login JupyterHub"}}
4 -=== ===
4 +=== ===
5 5  
6 6  {{view-file att--filename="tmp.mp4" height="150"/}}
7 7  {{/info}}
8 8  
9 +\\
10 +
9 9  {{info}}
10 10  === There are different options that help you to work with the FLASH HDF5 data in Python ===
11 11  
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12 12  * The currently developed option for large data sets: [[the FAB package>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]] ... see below
13 13  * and for smaller projects:  (% class="Object" %)[[https:~~/~~/gitlab.desy.de/christopher.passow/flash-daq-hdf>>url:https://gitlab.desy.de/christopher.passow/flash-daq-hdf||shape="rect"]]
14 14  
15 -(% class="Object" %)See also the collection of Demo data and sample scripts : [[doc:FS-FLASH USER tmp.Data Acquisition and controls 1.DAQ and controls overview.Offline data analysis (DAQ).Collection of HDF5 sample data from different beamlines.WebHome]]
17 +(% class="Object" %)See also the collection of Demo data and sample scripts : [[doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).Collection of HDF5 sample data from different beamlines.WebHome]]
16 16  {{/info}}
17 17  
20 +\\
18 18  
19 19  [[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
20 20  
24 +\\
25 +
21 21  {{expand title="older ideas ..."}}
22 22  (% class="Object" %)(object oriented) [[https:~~/~~/gitlab.desy.de/christopher.passow/fdh-builder>>url:https://gitlab.desy.de/christopher.passow/fdh-builder.git||shape="rect"]]
23 23  
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27 27  
28 28  (% class="task-list" %)
29 29  (((
30 -{{task reference="/Tasks/Task_18" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
31 -Short descriptions including Links:   → as Text
32 -\\
35 +{{task reference="/Tasks/Task_18" status="InProgress"}}
36 +Short descriptions including Links:   → as Text\\
37 +
38 +(% class="task-list" %)
39 +(((
40 +
41 +
42 +{{task reference="/Tasks/Task_19" status="InProgress"}}
43 +GPFS
33 33  {{/task}}
45 +
46 +{{task reference="/Tasks/Task_40" status="InProgress"}}
47 +Access rights
48 +{{/task}}
49 +
50 +{{task reference="/Tasks/Task_41" status="InProgress"}}
51 +Gamma Portal
52 +{{/task}}
53 +
54 +{{task reference="/Tasks/Task_42" status="InProgress"}}
55 +Maxwell
56 +{{/task}}
57 +
58 +{{task reference="/Tasks/Task_20" status="InProgress"}}
59 +JupyterHub
60 +{{/task}}
61 +
62 +{{task reference="/Tasks/Task_21" status="InProgress"}}
63 +conda ?
64 +{{/task}}
65 +
66 +{{task reference="/Tasks/Task_36" status="InProgress"}}
67 +explain install from channel instead of fixed environment, but can use environment file from example repository
68 +{{/task}}
34 34  )))
70 +{{/task}}
71 +)))
35 35  
73 +\\
36 36  
37 37  (% class="task-list" %)
38 38  (((
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43 43  (((
44 44  
45 45  
46 -{{task reference="/Tasks/Task_23" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
84 +{{task reference="/Tasks/Task_23" status="InProgress"}}
47 47  channel  (where to host?)
48 48  {{/task}}
49 49  
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54 54  {{/task}}
55 55  )))
56 56  
95 +\\
57 57  
58 58  (% class="task-list" %)
59 59  (((
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71 71  {{/task}}
72 72  )))
73 73  
113 +\\
74 74  
75 75  (% class="task-list" %)
76 76  (((
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88 88  {{/task}}
89 89  )))
90 90  
131 +\\
91 91  
92 92  (% class="task-list" %)
93 93  (((
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110 110  use slix
111 111  {{/task}}
112 112  
113 -{{task reference="/Tasks/Task_33" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
154 +{{task reference="/Tasks/Task_33" status="InProgress"}}
114 114  use hdfview plugin in jupterLab
115 115  {{/task}}
116 116  
117 -{{task reference="/Tasks/Task_34" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
158 +{{task reference="/Tasks/Task_34" status="InProgress"}}
118 118  create conda env with flashh5
119 119  {{/task}}
120 120  )))
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121 121  {{/task}}
122 122  )))
123 123  
165 +\\
124 124  
167 +\\
125 125  
126 126  ----
127 127  
128 128  ==== under review ====
129 129  
173 +\\
130 130  
131 131  {{code language="bash"}}
132 132  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
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143 143  ## delete from: /home/$USER/.local/share/jupyter/kernels/
144 144  {{/code}}
145 145  
146 -{{code language="py" title="
147 -moved to repository?"}}
190 +\\
191 +
192 +{{code language="py" title="moved to repository?"}}
148 148  class RunDirectory:
149 149  
150 150   def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
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189 189  # run.to_xarray(daq_map)
190 190  {{/code}}
191 191  
237 +\\
192 192  
193 -
239 +\\
194 194  {{/expand}}