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Last modified by makuadm on 2026-01-07 06:21
From version 52.1
edited by makuadm
on 2026-01-07 06:21
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_31.WebHome] has been updated!
To version 30.1
edited by cpassow
on 2022-04-06 16:53
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1 -FLASHUSER.Offline data analysis (DAQ).WebHome
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1 -XWiki.makuadm
1 +XWiki.cpassow
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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="TEST - 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 +\\
20 20  
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"]]
23 -
24 24  ----
25 25  
26 26  === TODO ===
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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 -\\
23 +{{task reference="/Tasks/Task_18" status="InProgress"}}
24 +Short descriptions including Links:   → as Text\\
25 +
26 +(% class="task-list" %)
27 +(((
28 +
29 +
30 +{{task reference="/Tasks/Task_19" status="InProgress"}}
31 +GPFS
33 33  {{/task}}
33 +
34 +{{task reference="/Tasks/Task_40" status="InProgress"}}
35 +Access rights
36 +{{/task}}
37 +
38 +{{task reference="/Tasks/Task_41" status="InProgress"}}
39 +Gamma Portal
40 +{{/task}}
41 +
42 +{{task reference="/Tasks/Task_42" status="InProgress"}}
43 +Maxwell
44 +{{/task}}
45 +
46 +{{task reference="/Tasks/Task_20" status="InProgress"}}
47 +JupyterHub
48 +{{/task}}
49 +
50 +{{task reference="/Tasks/Task_21" status="InProgress"}}
51 +conda ?
52 +{{/task}}
53 +
54 +{{task reference="/Tasks/Task_36" status="InProgress"}}
55 +explain install from channel instead of fixed environment, but can use environment file from example repository
56 +{{/task}}
34 34  )))
58 +{{/task}}
59 +)))
35 35  
61 +\\
36 36  
37 37  (% class="task-list" %)
38 38  (((
39 -{{task reference="/Tasks/Task_22" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
65 +{{task reference="/Tasks/Task_22" status="InProgress"}}
40 40  distribution
41 -\\
67 +
68 +(% class="task-list" %)
69 +(((
70 +
71 +
72 +{{task reference="/Tasks/Task_23" status="InProgress"}}
73 +channel  (where to host?)
42 42  {{/task}}
75 +
76 +{{task reference="/Tasks/Task_24" status="InProgress"}}
77 +environment file (repository with examples)
78 +{{/task}}
43 43  )))
80 +{{/task}}
81 +)))
44 44  
83 +\\
45 45  
46 46  (% class="task-list" %)
47 47  (((
48 -{{task reference="/Tasks/Task_25" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
87 +{{task reference="/Tasks/Task_25" status="InProgress"}}
49 49  Documentation
50 -\\
89 +
90 +(% class="task-list" %)
91 +(((
92 +
93 +
94 +{{task reference="/Tasks/Task_26" status="InProgress"}}
95 +here VS repository VS sphinx
51 51  {{/task}}
52 52  )))
98 +{{/task}}
99 +)))
53 53  
101 +\\
54 54  
55 55  (% class="task-list" %)
56 56  (((
57 -{{task reference="/Tasks/Task_27" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
105 +{{task reference="/Tasks/Task_27" status="InProgress"}}
58 58  Binder
59 -\\
107 +
108 +(% class="task-list" %)
109 +(((
110 +
111 +
112 +{{task reference="/Tasks/Task_28" status="InProgress"}}
113 +examples with Stefan
60 60  {{/task}}
61 61  )))
116 +{{/task}}
117 +)))
62 62  
119 +\\
63 63  
64 64  (% class="task-list" %)
65 65  (((
66 -{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
123 +{{task reference="/Tasks/Task_29" status="InProgress"}}
67 67  Screencast
68 -\\
125 +
126 +(% class="task-list" %)
127 +(((
128 +
129 +
130 +{{task reference="/Tasks/Task_30" status="InProgress"}}
131 +login in jupyter hub
69 69  {{/task}}
133 +
134 +{{task reference="/Tasks/Task_31" status="InProgress"}}
135 +login maxwell display
136 +{{/task}}
137 +
138 +{{task reference="/Tasks/Task_32" status="InProgress"}}
139 +use slix
140 +{{/task}}
141 +
142 +{{task reference="/Tasks/Task_33" status="InProgress"}}
143 +use hdfview plugin in jupterLab
144 +{{/task}}
145 +
146 +{{task reference="/Tasks/Task_34" status="InProgress"}}
147 +create conda env with flashh5
148 +{{/task}}
70 70  )))
150 +{{/task}}
151 +)))
71 71  
153 +\\
72 72  
155 +\\
73 73  
74 74  ----
75 75  
76 76  ==== under review ====
77 77  
161 +\\
78 78  
79 79  {{code language="bash"}}
80 80  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
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91 91  ## delete from: /home/$USER/.local/share/jupyter/kernels/
92 92  {{/code}}
93 93  
94 -{{code language="py" title="
95 -moved to repository?"}}
178 +\\
179 +
180 +{{code language="py" title="moved to repository?"}}
96 96  class RunDirectory:
97 97  
98 98   def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
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137 137  # run.to_xarray(daq_map)
138 138  {{/code}}
139 139  
225 +\\
140 140  
141 -
142 -{{/expand}}
227 +\\
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