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Last modified by makuadm on 2026-01-07 06:21
From version 32.1
edited by sndueste
on 2022-10-27 11:19
Change comment: There is no comment for this version
To version 46.1
edited by makuadm
on 2026-01-06 23:43
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_23.WebHome] has been updated!

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1 +FLASHUSER.Offline data analysis (DAQ).WebHome
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1 -XWiki.sndueste
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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="TEST - 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 -\\
19 +[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
16 16  
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 +
17 17  ----
18 18  
19 19  === TODO ===
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20 20  
21 21  (% class="task-list" %)
22 22  (((
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
30 +{{task reference="/Tasks/Task_18" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
31 +Short descriptions including Links:   → as Text
32 +\\
32 32  {{/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}}
57 57  )))
58 -{{/task}}
59 -)))
60 60  
61 -\\
62 62  
63 63  (% class="task-list" %)
64 64  (((
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69 69  (((
70 70  
71 71  
72 -{{task reference="/Tasks/Task_23" status="InProgress"}}
46 +{{task reference="/Tasks/Task_23" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
73 73  channel  (where to host?)
74 74  {{/task}}
75 75  
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80 80  {{/task}}
81 81  )))
82 82  
83 -\\
84 84  
85 85  (% class="task-list" %)
86 86  (((
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98 98  {{/task}}
99 99  )))
100 100  
101 -\\
102 102  
103 103  (% class="task-list" %)
104 104  (((
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116 116  {{/task}}
117 117  )))
118 118  
119 -\\
120 120  
121 121  (% class="task-list" %)
122 122  (((
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139 139  use slix
140 140  {{/task}}
141 141  
142 -{{task reference="/Tasks/Task_33" status="InProgress"}}
113 +{{task reference="/Tasks/Task_33" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
143 143  use hdfview plugin in jupterLab
144 144  {{/task}}
145 145  
146 -{{task reference="/Tasks/Task_34" status="InProgress"}}
117 +{{task reference="/Tasks/Task_34" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
147 147  create conda env with flashh5
148 148  {{/task}}
149 149  )))
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150 150  {{/task}}
151 151  )))
152 152  
153 -\\
154 154  
155 -\\
156 156  
157 157  ----
158 158  
159 159  ==== under review ====
160 160  
161 -\\
162 162  
163 163  {{code language="bash"}}
164 164  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
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175 175  ## delete from: /home/$USER/.local/share/jupyter/kernels/
176 176  {{/code}}
177 177  
178 -\\
179 -
180 -{{code language="py" title="moved to repository?"}}
146 +{{code language="py" title="
147 +moved to repository?"}}
181 181  class RunDirectory:
182 182  
183 183   def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
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222 222  # run.to_xarray(daq_map)
223 223  {{/code}}
224 224  
225 -\\
226 226  
227 -\\
193 +
194 +{{/expand}}
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