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Last modified by makuadm on 2026-01-07 06:21
From version 50.1
edited by makuadm
on 2026-01-07 03:06
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_25.WebHome] has been updated!
To version 36.1
edited by sndueste
on 2023-09-29 11:07
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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 +
15 +\\
16 +
9 9  {{info}}
10 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
18 +=== 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"]]
20 +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]]
22 +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  
25 +\\
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  
29 +\\
30 +
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"]]
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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 -\\
40 +{{task reference="/Tasks/Task_18" status="InProgress"}}
41 +Short descriptions including Links:   → as Text\\
42 +
43 +(% class="task-list" %)
44 +(((
45 +
46 +
47 +{{task reference="/Tasks/Task_19" status="InProgress"}}
48 +GPFS
33 33  {{/task}}
50 +
51 +{{task reference="/Tasks/Task_40" status="InProgress"}}
52 +Access rights
53 +{{/task}}
54 +
55 +{{task reference="/Tasks/Task_41" status="InProgress"}}
56 +Gamma Portal
57 +{{/task}}
58 +
59 +{{task reference="/Tasks/Task_42" status="InProgress"}}
60 +Maxwell
61 +{{/task}}
62 +
63 +{{task reference="/Tasks/Task_20" status="InProgress"}}
64 +JupyterHub
65 +{{/task}}
66 +
67 +{{task reference="/Tasks/Task_21" status="InProgress"}}
68 +conda ?
69 +{{/task}}
70 +
71 +{{task reference="/Tasks/Task_36" status="InProgress"}}
72 +explain install from channel instead of fixed environment, but can use environment file from example repository
73 +{{/task}}
34 34  )))
75 +{{/task}}
76 +)))
35 35  
78 +\\
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=""}}
89 +{{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  
100 +\\
57 57  
58 58  (% class="task-list" %)
59 59  (((
60 -{{task reference="/Tasks/Task_25" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
104 +{{task reference="/Tasks/Task_25" status="InProgress"}}
61 61  Documentation
62 -\\
106 +
107 +(% class="task-list" %)
108 +(((
109 +
110 +
111 +{{task reference="/Tasks/Task_26" status="InProgress"}}
112 +here VS repository VS sphinx
63 63  {{/task}}
64 64  )))
115 +{{/task}}
116 +)))
65 65  
118 +\\
66 66  
67 67  (% class="task-list" %)
68 68  (((
69 -{{task reference="/Tasks/Task_27" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
122 +{{task reference="/Tasks/Task_27" status="InProgress"}}
70 70  Binder
71 -\\
124 +
125 +(% class="task-list" %)
126 +(((
127 +
128 +
129 +{{task reference="/Tasks/Task_28" status="InProgress"}}
130 +examples with Stefan
72 72  {{/task}}
73 73  )))
133 +{{/task}}
134 +)))
74 74  
136 +\\
75 75  
76 76  (% class="task-list" %)
77 77  (((
78 -{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
140 +{{task reference="/Tasks/Task_29" status="InProgress"}}
79 79  Screencast
80 -\\
142 +
143 +(% class="task-list" %)
144 +(((
145 +
146 +
147 +{{task reference="/Tasks/Task_30" status="InProgress"}}
148 +login in jupyter hub
81 81  {{/task}}
150 +
151 +{{task reference="/Tasks/Task_31" status="InProgress"}}
152 +login maxwell display
153 +{{/task}}
154 +
155 +{{task reference="/Tasks/Task_32" status="InProgress"}}
156 +use slix
157 +{{/task}}
158 +
159 +{{task reference="/Tasks/Task_33" status="InProgress"}}
160 +use hdfview plugin in jupterLab
161 +{{/task}}
162 +
163 +{{task reference="/Tasks/Task_34" status="InProgress"}}
164 +create conda env with flashh5
165 +{{/task}}
82 82  )))
167 +{{/task}}
168 +)))
83 83  
170 +\\
84 84  
172 +\\
85 85  
86 86  ----
87 87  
88 88  ==== under review ====
89 89  
178 +\\
90 90  
91 91  {{code language="bash"}}
92 92  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
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103 103  ## delete from: /home/$USER/.local/share/jupyter/kernels/
104 104  {{/code}}
105 105  
106 -{{code language="py" title="
107 -moved to repository?"}}
195 +\\
196 +
197 +{{code language="py" title="moved to repository?"}}
108 108  class RunDirectory:
109 109  
110 110   def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
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149 149  # run.to_xarray(daq_map)
150 150  {{/code}}
151 151  
242 +\\
152 152  
153 -
244 +\\
154 154  {{/expand}}
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