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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 34.1
edited by sndueste
on 2023-09-28 16:52
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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] on the GPFS file system[link]. The access rights[link to ACLs] are linked to the user's DESY account and can be managed by the PI via the GAMMA portal[link]. 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[link], Maxwell-Display Server[link] or JuyterHub[link]. We recommmend using the JupyterHub for data exploration and the SLURM resources[link] for high performances computing.
2 2  
3 -{{info title="How to login JupyterHub"}}
4 -=== ===
3 +For simplified acccess we provide a conda module flashh5[link] which can be installed in a personal conda environment[link] on the Maxwell Cluster. Example on the usage can be found here [link - repo + binder]
5 5  
6 -{{view-file att--filename="tmp.mp4" height="150"/}}
7 -{{/info}}
5 +\\
8 8  
9 -{{info}}
10 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
7 +{{expand title="How to login JupyterHub"}}
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 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 -{{/info}}
10 +{{view-file att--filename="tmp.mp4" height="250"/}}
11 +{{/expand}}
17 17  
13 +\\
18 18  
19 -[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
15 +link to Repos and Fab
20 20  
17 +\\
18 +
19 +\\
20 +
21 +\\
22 +
21 21  {{expand title="older ideas ..."}}
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"]]
24 +\\
23 23  
24 24  ----
25 25  
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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 -\\
32 +{{task reference="/Tasks/Task_18" status="InProgress"}}
33 +Short descriptions including Links:   → as Text\\
34 +
35 +(% class="task-list" %)
36 +(((
37 +
38 +
39 +{{task reference="/Tasks/Task_19" status="InProgress"}}
40 +GPFS
33 33  {{/task}}
42 +
43 +{{task reference="/Tasks/Task_40" status="InProgress"}}
44 +Access rights
45 +{{/task}}
46 +
47 +{{task reference="/Tasks/Task_41" status="InProgress"}}
48 +Gamma Portal
49 +{{/task}}
50 +
51 +{{task reference="/Tasks/Task_42" status="InProgress"}}
52 +Maxwell
53 +{{/task}}
54 +
55 +{{task reference="/Tasks/Task_20" status="InProgress"}}
56 +JupyterHub
57 +{{/task}}
58 +
59 +{{task reference="/Tasks/Task_21" status="InProgress"}}
60 +conda ?
61 +{{/task}}
62 +
63 +{{task reference="/Tasks/Task_36" status="InProgress"}}
64 +explain install from channel instead of fixed environment, but can use environment file from example repository
65 +{{/task}}
34 34  )))
67 +{{/task}}
68 +)))
35 35  
70 +\\
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=""}}
81 +{{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  
92 +\\
57 57  
58 58  (% class="task-list" %)
59 59  (((
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71 71  {{/task}}
72 72  )))
73 73  
110 +\\
74 74  
75 75  (% class="task-list" %)
76 76  (((
77 -{{task reference="/Tasks/Task_27" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
114 +{{task reference="/Tasks/Task_27" status="InProgress"}}
78 78  Binder
79 -\\
116 +
117 +(% class="task-list" %)
118 +(((
119 +
120 +
121 +{{task reference="/Tasks/Task_28" status="InProgress"}}
122 +examples with Stefan
80 80  {{/task}}
81 81  )))
125 +{{/task}}
126 +)))
82 82  
128 +\\
83 83  
84 84  (% class="task-list" %)
85 85  (((
86 -{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
132 +{{task reference="/Tasks/Task_29" status="InProgress"}}
87 87  Screencast
88 -\\
134 +
135 +(% class="task-list" %)
136 +(((
137 +
138 +
139 +{{task reference="/Tasks/Task_30" status="InProgress"}}
140 +login in jupyter hub
89 89  {{/task}}
142 +
143 +{{task reference="/Tasks/Task_31" status="InProgress"}}
144 +login maxwell display
145 +{{/task}}
146 +
147 +{{task reference="/Tasks/Task_32" status="InProgress"}}
148 +use slix
149 +{{/task}}
150 +
151 +{{task reference="/Tasks/Task_33" status="InProgress"}}
152 +use hdfview plugin in jupterLab
153 +{{/task}}
154 +
155 +{{task reference="/Tasks/Task_34" status="InProgress"}}
156 +create conda env with flashh5
157 +{{/task}}
90 90  )))
159 +{{/task}}
160 +)))
91 91  
162 +\\
92 92  
164 +\\
93 93  
94 94  ----
95 95  
96 96  ==== under review ====
97 97  
170 +\\
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?"}}
187 +\\
188 +
189 +{{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  
234 +\\
160 160  
161 -
236 +\\
162 162  {{/expand}}
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