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Last modified by makuadm on 2026-01-07 06:21
From version 49.1
edited by makuadm
on 2026-01-07 01:26
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_27.WebHome] has been updated!
To version 38.1
edited by sndueste
on 2023-09-29 11:15
Change comment: There is no comment for this version

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1 -FLASHUSER.Offline data analysis (DAQ).WebHome
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1 -XWiki.makuadm
1 +XWiki.sndueste
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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 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
12 +=== There are different options that help you to work with the FLASH HDF5 data in Python ===
11 11  
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 -* 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 +The currently developed option for large data sets: [[the FAB package>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]] ... see below
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]]
16 +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"]]
16 16  {{/info}}
17 17  
19 +\\
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  
23 +\\
24 +
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 -\\
34 +{{task reference="/Tasks/Task_18" status="InProgress"}}
35 +Short descriptions including Links:   → as Text\\
36 +
37 +(% class="task-list" %)
38 +(((
39 +
40 +
41 +{{task reference="/Tasks/Task_19" status="InProgress"}}
42 +GPFS
33 33  {{/task}}
44 +
45 +{{task reference="/Tasks/Task_40" status="InProgress"}}
46 +Access rights
47 +{{/task}}
48 +
49 +{{task reference="/Tasks/Task_41" status="InProgress"}}
50 +Gamma Portal
51 +{{/task}}
52 +
53 +{{task reference="/Tasks/Task_42" status="InProgress"}}
54 +Maxwell
55 +{{/task}}
56 +
57 +{{task reference="/Tasks/Task_20" status="InProgress"}}
58 +JupyterHub
59 +{{/task}}
60 +
61 +{{task reference="/Tasks/Task_21" status="InProgress"}}
62 +conda ?
63 +{{/task}}
64 +
65 +{{task reference="/Tasks/Task_36" status="InProgress"}}
66 +explain install from channel instead of fixed environment, but can use environment file from example repository
67 +{{/task}}
34 34  )))
69 +{{/task}}
70 +)))
35 35  
72 +\\
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=""}}
83 +{{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  
94 +\\
57 57  
58 58  (% class="task-list" %)
59 59  (((
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71 71  {{/task}}
72 72  )))
73 73  
112 +\\
74 74  
75 75  (% class="task-list" %)
76 76  (((
77 -{{task reference="/Tasks/Task_27" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
116 +{{task reference="/Tasks/Task_27" status="InProgress"}}
78 78  Binder
79 -\\
118 +
119 +(% class="task-list" %)
120 +(((
121 +
122 +
123 +{{task reference="/Tasks/Task_28" status="InProgress"}}
124 +examples with Stefan
80 80  {{/task}}
81 81  )))
127 +{{/task}}
128 +)))
82 82  
130 +\\
83 83  
84 84  (% class="task-list" %)
85 85  (((
86 -{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
134 +{{task reference="/Tasks/Task_29" status="InProgress"}}
87 87  Screencast
88 -\\
136 +
137 +(% class="task-list" %)
138 +(((
139 +
140 +
141 +{{task reference="/Tasks/Task_30" status="InProgress"}}
142 +login in jupyter hub
89 89  {{/task}}
144 +
145 +{{task reference="/Tasks/Task_31" status="InProgress"}}
146 +login maxwell display
147 +{{/task}}
148 +
149 +{{task reference="/Tasks/Task_32" status="InProgress"}}
150 +use slix
151 +{{/task}}
152 +
153 +{{task reference="/Tasks/Task_33" status="InProgress"}}
154 +use hdfview plugin in jupterLab
155 +{{/task}}
156 +
157 +{{task reference="/Tasks/Task_34" status="InProgress"}}
158 +create conda env with flashh5
159 +{{/task}}
90 90  )))
161 +{{/task}}
162 +)))
91 91  
164 +\\
92 92  
166 +\\
93 93  
94 94  ----
95 95  
96 96  ==== under review ====
97 97  
172 +\\
98 98  
99 99  {{code language="bash"}}
100 100  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
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111 111  ## delete from: /home/$USER/.local/share/jupyter/kernels/
112 112  {{/code}}
113 113  
114 -{{code language="py" title="
115 -moved to repository?"}}
189 +\\
190 +
191 +{{code language="py" title="moved to repository?"}}
116 116  class RunDirectory:
117 117  
118 118   def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
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157 157  # run.to_xarray(daq_map)
158 158  {{/code}}
159 159  
236 +\\
160 160  
161 -
238 +\\
162 162  {{/expand}}
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