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Last modified by makuadm on 2026-01-07 06:21
From version 37.1
edited by sndueste
on 2023-09-29 11:13
Change comment: There is no comment for this version
To version 48.1
edited by makuadm
on 2026-01-07 00:43
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_29.WebHome] has been updated!

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1 +FLASHUSER.Offline data analysis (DAQ).WebHome
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1 -XWiki.sndueste
1 +XWiki.makuadm
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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.
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.
2 2  
3 -\\
3 +{{info title="How to login JupyterHub"}}
4 +=== ===
4 4  
5 -{{expand title="How to login JupyterHub"}}
6 +{{view-file att--filename="tmp.mp4" height="150"/}}
7 +{{/info}}
6 6  
7 -
8 -{{view-file att--filename="tmp.mp4" height="250"/}}
9 -{{/expand}}
10 -
11 -\\
12 -
13 -\\
14 -
15 15  {{info}}
16 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
10 +=== There are different options that help you to work with the FLASH HDF5 data in Python ===
17 17  
18 -The currently developed option for large data sets: [[the FAB package>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]] ... see below
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"]]
19 19  
20 -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"]]
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]]
21 21  {{/info}}
22 22  
23 -\\
24 24  
25 25  [[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
26 26  
27 -\\
28 -
29 29  {{expand title="older ideas ..."}}
30 30  (% 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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35 35  
36 36  (% class="task-list" %)
37 37  (((
38 -{{task reference="/Tasks/Task_18" status="InProgress"}}
39 -Short descriptions including Links:   → as Text\\
40 -
41 -(% class="task-list" %)
42 -(((
43 -
44 -
45 -{{task reference="/Tasks/Task_19" status="InProgress"}}
46 -GPFS
30 +{{task reference="/Tasks/Task_18" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
31 +Short descriptions including Links:   → as Text
32 +\\
47 47  {{/task}}
48 -
49 -{{task reference="/Tasks/Task_40" status="InProgress"}}
50 -Access rights
51 -{{/task}}
52 -
53 -{{task reference="/Tasks/Task_41" status="InProgress"}}
54 -Gamma Portal
55 -{{/task}}
56 -
57 -{{task reference="/Tasks/Task_42" status="InProgress"}}
58 -Maxwell
59 -{{/task}}
60 -
61 -{{task reference="/Tasks/Task_20" status="InProgress"}}
62 -JupyterHub
63 -{{/task}}
64 -
65 -{{task reference="/Tasks/Task_21" status="InProgress"}}
66 -conda ?
67 -{{/task}}
68 -
69 -{{task reference="/Tasks/Task_36" status="InProgress"}}
70 -explain install from channel instead of fixed environment, but can use environment file from example repository
71 -{{/task}}
72 72  )))
73 -{{/task}}
74 -)))
75 75  
76 -\\
77 77  
78 78  (% class="task-list" %)
79 79  (((
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84 84  (((
85 85  
86 86  
87 -{{task reference="/Tasks/Task_23" status="InProgress"}}
46 +{{task reference="/Tasks/Task_23" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
88 88  channel  (where to host?)
89 89  {{/task}}
90 90  
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95 95  {{/task}}
96 96  )))
97 97  
98 -\\
99 99  
100 100  (% class="task-list" %)
101 101  (((
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113 113  {{/task}}
114 114  )))
115 115  
116 -\\
117 117  
118 118  (% class="task-list" %)
119 119  (((
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131 131  {{/task}}
132 132  )))
133 133  
134 -\\
135 135  
136 136  (% class="task-list" %)
137 137  (((
138 -{{task reference="/Tasks/Task_29" status="InProgress"}}
94 +{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
139 139  Screencast
140 -
141 -(% class="task-list" %)
142 -(((
143 -
144 -
145 -{{task reference="/Tasks/Task_30" status="InProgress"}}
146 -login in jupyter hub
96 +\\
147 147  {{/task}}
148 -
149 -{{task reference="/Tasks/Task_31" status="InProgress"}}
150 -login maxwell display
151 -{{/task}}
152 -
153 -{{task reference="/Tasks/Task_32" status="InProgress"}}
154 -use slix
155 -{{/task}}
156 -
157 -{{task reference="/Tasks/Task_33" status="InProgress"}}
158 -use hdfview plugin in jupterLab
159 -{{/task}}
160 -
161 -{{task reference="/Tasks/Task_34" status="InProgress"}}
162 -create conda env with flashh5
163 -{{/task}}
164 164  )))
165 -{{/task}}
166 -)))
167 167  
168 -\\
169 169  
170 -\\
171 171  
172 172  ----
173 173  
174 174  ==== under review ====
175 175  
176 -\\
177 177  
178 178  {{code language="bash"}}
179 179  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
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190 190  ## delete from: /home/$USER/.local/share/jupyter/kernels/
191 191  {{/code}}
192 192  
193 -\\
194 -
195 -{{code language="py" title="moved to repository?"}}
122 +{{code language="py" title="
123 +moved to repository?"}}
196 196  class RunDirectory:
197 197  
198 198   def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
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237 237  # run.to_xarray(daq_map)
238 238  {{/code}}
239 239  
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241 241  
242 -\\
169 +
243 243  {{/expand}}
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