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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 41.2
edited by sndueste
on 2025-02-05 11:21
Change comment: Update document after refactoring.

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1 -FLASHUSER.Offline data analysis (DAQ).WebHome
1 +FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).WebHome
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1 -XWiki.makuadm
1 +XWiki.sndueste
Content
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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 10  === There are different options that help you to work with the FLASH HDF5 data in Python ===
11 11  
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12 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 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]]
17 +(% class="Object" %)See also the collection of Demo data and sample scripts : [[doc:FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).Collection of HDF5 sample data from different beamlines.WebHome]]
16 16  {{/info}}
17 17  
20 +\\
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  
24 +\\
25 +
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 -\\
35 +{{task reference="/Tasks/Task_18" status="InProgress"}}
36 +Short descriptions including Links:   → as Text\\
37 +
38 +(% class="task-list" %)
39 +(((
40 +
41 +
42 +{{task reference="/Tasks/Task_19" status="InProgress"}}
43 +GPFS
33 33  {{/task}}
45 +
46 +{{task reference="/Tasks/Task_40" status="InProgress"}}
47 +Access rights
48 +{{/task}}
49 +
50 +{{task reference="/Tasks/Task_41" status="InProgress"}}
51 +Gamma Portal
52 +{{/task}}
53 +
54 +{{task reference="/Tasks/Task_42" status="InProgress"}}
55 +Maxwell
56 +{{/task}}
57 +
58 +{{task reference="/Tasks/Task_20" status="InProgress"}}
59 +JupyterHub
60 +{{/task}}
61 +
62 +{{task reference="/Tasks/Task_21" status="InProgress"}}
63 +conda ?
64 +{{/task}}
65 +
66 +{{task reference="/Tasks/Task_36" status="InProgress"}}
67 +explain install from channel instead of fixed environment, but can use environment file from example repository
68 +{{/task}}
34 34  )))
70 +{{/task}}
71 +)))
35 35  
73 +\\
36 36  
37 37  (% class="task-list" %)
38 38  (((
39 -{{task reference="/Tasks/Task_22" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
77 +{{task reference="/Tasks/Task_22" status="InProgress"}}
40 40  distribution
41 -\\
79 +
80 +(% class="task-list" %)
81 +(((
82 +
83 +
84 +{{task reference="/Tasks/Task_23" status="InProgress"}}
85 +channel  (where to host?)
42 42  {{/task}}
87 +
88 +{{task reference="/Tasks/Task_24" status="InProgress"}}
89 +environment file (repository with examples)
90 +{{/task}}
43 43  )))
92 +{{/task}}
93 +)))
44 44  
95 +\\
45 45  
46 46  (% class="task-list" %)
47 47  (((
48 -{{task reference="/Tasks/Task_25" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
99 +{{task reference="/Tasks/Task_25" status="InProgress"}}
49 49  Documentation
50 -\\
101 +
102 +(% class="task-list" %)
103 +(((
104 +
105 +
106 +{{task reference="/Tasks/Task_26" status="InProgress"}}
107 +here VS repository VS sphinx
51 51  {{/task}}
52 52  )))
110 +{{/task}}
111 +)))
53 53  
113 +\\
54 54  
55 55  (% class="task-list" %)
56 56  (((
57 -{{task reference="/Tasks/Task_27" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
117 +{{task reference="/Tasks/Task_27" status="InProgress"}}
58 58  Binder
59 -\\
119 +
120 +(% class="task-list" %)
121 +(((
122 +
123 +
124 +{{task reference="/Tasks/Task_28" status="InProgress"}}
125 +examples with Stefan
60 60  {{/task}}
61 61  )))
128 +{{/task}}
129 +)))
62 62  
131 +\\
63 63  
64 64  (% class="task-list" %)
65 65  (((
66 -{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
135 +{{task reference="/Tasks/Task_29" status="InProgress"}}
67 67  Screencast
68 -\\
137 +
138 +(% class="task-list" %)
139 +(((
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141 +
142 +{{task reference="/Tasks/Task_30" status="InProgress"}}
143 +login in jupyter hub
69 69  {{/task}}
145 +
146 +{{task reference="/Tasks/Task_31" status="InProgress"}}
147 +login maxwell display
148 +{{/task}}
149 +
150 +{{task reference="/Tasks/Task_32" status="InProgress"}}
151 +use slix
152 +{{/task}}
153 +
154 +{{task reference="/Tasks/Task_33" status="InProgress"}}
155 +use hdfview plugin in jupterLab
156 +{{/task}}
157 +
158 +{{task reference="/Tasks/Task_34" status="InProgress"}}
159 +create conda env with flashh5
160 +{{/task}}
70 70  )))
162 +{{/task}}
163 +)))
71 71  
165 +\\
72 72  
167 +\\
73 73  
74 74  ----
75 75  
76 76  ==== under review ====
77 77  
173 +\\
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?"}}
190 +\\
191 +
192 +{{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  
237 +\\
140 140  
141 -
239 +\\
142 142  {{/expand}}