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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 35.1
edited by sndueste
on 2023-09-28 16:54
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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  
7 +{{expand title="How to login JupyterHub"}}
8 +
9 +
10 +{{view-file att--filename="tmp.mp4" height="250"/}}
11 +{{/expand}}
12 +
13 +\\
14 +
9 9  {{info}}
10 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
16 +=== Reference implementation (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"]]
18 +(imperative)  (% 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]]
20 +(% class="Object" %)(object oriented) [[https:~~/~~/gitlab.desy.de/christopher.passow/fdh-builder>>url:https://gitlab.desy.de/christopher.passow/fdh-builder.git||shape="rect"]]
21 +
22 +\\
16 16  {{/info}}
17 17  
25 +link to Repos and Fab
18 18  
19 -[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
27 +\\
20 20  
29 +\\
30 +
31 +\\
32 +
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"]]
34 +\\
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 -\\
42 +{{task reference="/Tasks/Task_18" status="InProgress"}}
43 +Short descriptions including Links:   → as Text\\
44 +
45 +(% class="task-list" %)
46 +(((
47 +
48 +
49 +{{task reference="/Tasks/Task_19" status="InProgress"}}
50 +GPFS
33 33  {{/task}}
52 +
53 +{{task reference="/Tasks/Task_40" status="InProgress"}}
54 +Access rights
55 +{{/task}}
56 +
57 +{{task reference="/Tasks/Task_41" status="InProgress"}}
58 +Gamma Portal
59 +{{/task}}
60 +
61 +{{task reference="/Tasks/Task_42" status="InProgress"}}
62 +Maxwell
63 +{{/task}}
64 +
65 +{{task reference="/Tasks/Task_20" status="InProgress"}}
66 +JupyterHub
67 +{{/task}}
68 +
69 +{{task reference="/Tasks/Task_21" status="InProgress"}}
70 +conda ?
71 +{{/task}}
72 +
73 +{{task reference="/Tasks/Task_36" status="InProgress"}}
74 +explain install from channel instead of fixed environment, but can use environment file from example repository
75 +{{/task}}
34 34  )))
77 +{{/task}}
78 +)))
35 35  
80 +\\
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=""}}
91 +{{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  
102 +\\
57 57  
58 58  (% class="task-list" %)
59 59  (((
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71 71  {{/task}}
72 72  )))
73 73  
120 +\\
74 74  
75 75  (% class="task-list" %)
76 76  (((
77 -{{task reference="/Tasks/Task_27" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
124 +{{task reference="/Tasks/Task_27" status="InProgress"}}
78 78  Binder
79 -\\
126 +
127 +(% class="task-list" %)
128 +(((
129 +
130 +
131 +{{task reference="/Tasks/Task_28" status="InProgress"}}
132 +examples with Stefan
80 80  {{/task}}
81 81  )))
135 +{{/task}}
136 +)))
82 82  
138 +\\
83 83  
84 84  (% class="task-list" %)
85 85  (((
86 -{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
142 +{{task reference="/Tasks/Task_29" status="InProgress"}}
87 87  Screencast
88 -\\
144 +
145 +(% class="task-list" %)
146 +(((
147 +
148 +
149 +{{task reference="/Tasks/Task_30" status="InProgress"}}
150 +login in jupyter hub
89 89  {{/task}}
152 +
153 +{{task reference="/Tasks/Task_31" status="InProgress"}}
154 +login maxwell display
155 +{{/task}}
156 +
157 +{{task reference="/Tasks/Task_32" status="InProgress"}}
158 +use slix
159 +{{/task}}
160 +
161 +{{task reference="/Tasks/Task_33" status="InProgress"}}
162 +use hdfview plugin in jupterLab
163 +{{/task}}
164 +
165 +{{task reference="/Tasks/Task_34" status="InProgress"}}
166 +create conda env with flashh5
167 +{{/task}}
90 90  )))
169 +{{/task}}
170 +)))
91 91  
172 +\\
92 92  
174 +\\
93 93  
94 94  ----
95 95  
96 96  ==== under review ====
97 97  
180 +\\
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?"}}
197 +\\
198 +
199 +{{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  
244 +\\
160 160  
161 -
246 +\\
162 162  {{/expand}}
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