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Last modified by makuadm on 2026-01-07 06:21
From version 34.1
edited by sndueste
on 2023-09-28 16:52
Change comment: There is no comment for this version
To 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!

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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] 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.
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 -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]
3 +{{info title="How to login JupyterHub"}}
4 +=== ===
4 4  
5 -\\
6 +{{view-file att--filename="tmp.mp4" height="150"/}}
7 +{{/info}}
6 6  
7 -{{expand title="How to login JupyterHub"}}
9 +{{info}}
10 +=== There are different options that help you to work with the FLASH HDF5 data in Python ===
8 8  
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"]]
9 9  
10 -{{view-file att--filename="tmp.mp4" height="250"/}}
11 -{{/expand}}
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}}
12 12  
13 -\\
14 14  
15 -link to Repos and Fab
19 +[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
16 16  
17 -\\
18 -
19 -\\
20 -
21 -\\
22 -
23 23  {{expand title="older ideas ..."}}
24 -\\
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"]]
25 25  
26 26  ----
27 27  
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29 29  
30 30  (% class="task-list" %)
31 31  (((
32 -{{task reference="/Tasks/Task_18" status="InProgress"}}
33 -Short descriptions including Links:   → as Text\\
34 -
35 -(% class="task-list" %)
36 -(((
37 -
38 -
39 -{{task reference="/Tasks/Task_19" status="InProgress"}}
40 -GPFS
30 +{{task reference="/Tasks/Task_18" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
31 +Short descriptions including Links:   → as Text
32 +\\
41 41  {{/task}}
42 -
43 -{{task reference="/Tasks/Task_40" status="InProgress"}}
44 -Access rights
45 -{{/task}}
46 -
47 -{{task reference="/Tasks/Task_41" status="InProgress"}}
48 -Gamma Portal
49 -{{/task}}
50 -
51 -{{task reference="/Tasks/Task_42" status="InProgress"}}
52 -Maxwell
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54 -
55 -{{task reference="/Tasks/Task_20" status="InProgress"}}
56 -JupyterHub
57 -{{/task}}
58 -
59 -{{task reference="/Tasks/Task_21" status="InProgress"}}
60 -conda ?
61 -{{/task}}
62 -
63 -{{task reference="/Tasks/Task_36" status="InProgress"}}
64 -explain install from channel instead of fixed environment, but can use environment file from example repository
65 -{{/task}}
66 66  )))
67 -{{/task}}
68 -)))
69 69  
70 -\\
71 71  
72 72  (% class="task-list" %)
73 73  (((
74 -{{task reference="/Tasks/Task_22" status="InProgress"}}
39 +{{task reference="/Tasks/Task_22" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
75 75  distribution
76 -
77 -(% class="task-list" %)
78 -(((
79 -
80 -
81 -{{task reference="/Tasks/Task_23" status="InProgress"}}
82 -channel  (where to host?)
41 +\\
83 83  {{/task}}
84 -
85 -{{task reference="/Tasks/Task_24" status="InProgress"}}
86 -environment file (repository with examples)
87 -{{/task}}
88 88  )))
89 -{{/task}}
90 -)))
91 91  
92 -\\
93 93  
94 94  (% class="task-list" %)
95 95  (((
96 -{{task reference="/Tasks/Task_25" status="InProgress"}}
48 +{{task reference="/Tasks/Task_25" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
97 97  Documentation
98 -
99 -(% class="task-list" %)
100 -(((
101 -
102 -
103 -{{task reference="/Tasks/Task_26" status="InProgress"}}
104 -here VS repository VS sphinx
50 +\\
105 105  {{/task}}
106 106  )))
107 -{{/task}}
108 -)))
109 109  
110 -\\
111 111  
112 112  (% class="task-list" %)
113 113  (((
114 -{{task reference="/Tasks/Task_27" status="InProgress"}}
57 +{{task reference="/Tasks/Task_27" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
115 115  Binder
116 -
117 -(% class="task-list" %)
118 -(((
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120 -
121 -{{task reference="/Tasks/Task_28" status="InProgress"}}
122 -examples with Stefan
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123 123  {{/task}}
124 124  )))
125 -{{/task}}
126 -)))
127 127  
128 -\\
129 129  
130 130  (% class="task-list" %)
131 131  (((
132 -{{task reference="/Tasks/Task_29" status="InProgress"}}
66 +{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
133 133  Screencast
134 -
135 -(% class="task-list" %)
136 -(((
137 -
138 -
139 -{{task reference="/Tasks/Task_30" status="InProgress"}}
140 -login in jupyter hub
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141 141  {{/task}}
142 -
143 -{{task reference="/Tasks/Task_31" status="InProgress"}}
144 -login maxwell display
145 -{{/task}}
146 -
147 -{{task reference="/Tasks/Task_32" status="InProgress"}}
148 -use slix
149 -{{/task}}
150 -
151 -{{task reference="/Tasks/Task_33" status="InProgress"}}
152 -use hdfview plugin in jupterLab
153 -{{/task}}
154 -
155 -{{task reference="/Tasks/Task_34" status="InProgress"}}
156 -create conda env with flashh5
157 -{{/task}}
158 158  )))
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160 -)))
161 161  
162 -\\
163 163  
164 -\\
165 165  
166 166  ----
167 167  
168 168  ==== under review ====
169 169  
170 -\\
171 171  
172 172  {{code language="bash"}}
173 173  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
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184 184  ## delete from: /home/$USER/.local/share/jupyter/kernels/
185 185  {{/code}}
186 186  
187 -\\
188 -
189 -{{code language="py" title="moved to repository?"}}
94 +{{code language="py" title="
95 +moved to repository?"}}
190 190  class RunDirectory:
191 191  
192 192   def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
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231 231  # run.to_xarray(daq_map)
232 232  {{/code}}
233 233  
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237 237  {{/expand}}
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