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Last modified by makuadm on 2026-01-07 06:21
From version 43.1
edited by makuadm
on 2026-01-06 20:39
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_18.WebHome] has been updated!
To version 20.1
edited by cpassow
on 2022-04-04 15:18
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Title
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1 -DEMO - Working with FLASH data
1 +DEMO - Documentation
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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 +(% style="list-style-type: square;" %)
2 +* Short descriptions including Links:   → as Text\\
3 +(% style="list-style-type: square;" %)
4 +** GPFS
5 +** JupyterHub
6 +** conda ?
2 2  
3 -{{info title="How to login JupyterHub"}}
4 -=== ===
8 +\\
5 5  
6 -{{view-file att--filename="tmp.mp4" height="150"/}}
7 -{{/info}}
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11 +* Links Repository
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13 +** including Method Description: Readme or Sphinx ?
8 8  
9 -{{info}}
10 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
15 +\\
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"]]
17 +(% style="list-style-type: square;" %)
18 +* Links to Binder
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}}
20 +\\
17 17  
22 +(% style="list-style-type: square;" %)
23 +* Screencast
18 18  
19 -[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
25 +\\
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"]]
27 +\\
23 23  
24 -----
29 +Questions:
25 25  
26 -=== TODO ===
31 +(% style="list-style-type: square;" %)
32 +* distribution\\
33 +(% style="list-style-type: square;" %)
34 +** channel
35 +** enviroment → as example for binder
27 27  
28 -(% class="task-list" %)
29 -(((
30 -{{task reference="/Tasks/Task_18" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
31 -Short descriptions including Links:   → as Text
32 -\\
33 -{{/task}}
34 -)))
37 +\\
35 35  
36 -
37 -(% class="task-list" %)
38 -(((
39 -{{task reference="/Tasks/Task_22" status="InProgress"}}
40 -distribution
41 -
42 -(% class="task-list" %)
43 -(((
44 -
45 -
46 -{{task reference="/Tasks/Task_23" status="InProgress"}}
47 -channel  (where to host?)
48 -{{/task}}
49 -
50 -{{task reference="/Tasks/Task_24" status="InProgress"}}
51 -environment file (repository with examples)
52 -{{/task}}
53 -)))
54 -{{/task}}
55 -)))
56 -
57 -
58 -(% class="task-list" %)
59 -(((
60 -{{task reference="/Tasks/Task_25" status="InProgress"}}
61 -Documentation
62 -
63 -(% class="task-list" %)
64 -(((
65 -
66 -
67 -{{task reference="/Tasks/Task_26" status="InProgress"}}
68 -here VS repository VS sphinx
69 -{{/task}}
70 -)))
71 -{{/task}}
72 -)))
73 -
74 -
75 -(% class="task-list" %)
76 -(((
77 -{{task reference="/Tasks/Task_27" status="InProgress"}}
78 -Binder
79 -
80 -(% class="task-list" %)
81 -(((
82 -
83 -
84 -{{task reference="/Tasks/Task_28" status="InProgress"}}
85 -examples with Stefan
86 -{{/task}}
87 -)))
88 -{{/task}}
89 -)))
90 -
91 -
92 -(% class="task-list" %)
93 -(((
94 -{{task reference="/Tasks/Task_29" status="InProgress"}}
95 -Screencast
96 -
97 -(% class="task-list" %)
98 -(((
99 -
100 -
101 -{{task reference="/Tasks/Task_30" status="InProgress"}}
102 -login in jupyter hub
103 -{{/task}}
104 -
105 -{{task reference="/Tasks/Task_31" status="InProgress"}}
106 -login maxwell display
107 -{{/task}}
108 -
109 -{{task reference="/Tasks/Task_32" status="InProgress"}}
110 -use slix
111 -{{/task}}
112 -
113 -{{task reference="/Tasks/Task_33" status="InProgress"}}
114 -use hdfview plugin in jupterLab
115 -{{/task}}
116 -
117 -{{task reference="/Tasks/Task_34" status="InProgress"}}
118 -create conda env with flashh5
119 -{{/task}}
120 -)))
121 -{{/task}}
122 -)))
123 -
124 -
125 -
126 -----
127 -
128 -==== under review ====
129 -
130 -
131 131  {{code language="bash"}}
132 132  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
133 133  source activate flashh5
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143 143  ## delete from: /home/$USER/.local/share/jupyter/kernels/
144 144  {{/code}}
145 145  
146 -{{code language="py" title="
147 -moved to repository?"}}
54 +\\
55 +
56 +{{code language="py" title="moved to repository?"}}
148 148  class RunDirectory:
149 149  
150 - def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
59 + def get_run_table(): # more or less information? RunComment | Number of Files
151 151   ...
152 152  
153 - def get_run(daq, run_number): # daq is not needed!
154 -
62 + def get_run(daq, run_number): # daq is not needed
155 155   ...
156 156  
157 157  
158 -class Run: # constructor optional without RunDirectory or use there self.path
66 +class Run:
159 159  
160 160   def get_files():
161 161   ...
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168 168  
169 169   def get_stop_time(): # which? | better as attribute?
170 170   ...
79 +
80 +### for following methods to restrict number of files or separate method
81 +### e.g. create_df(files)
171 171  
172 172   def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
173 173   ...
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184 184  run.to_series(daq_adr or daq_map) # on channel only?
185 185  run.to_array(daq_adr) # on channel only?
186 186  
187 -## interesting?
98 +## is this interesting?
188 188  # run.to_dask(daq_map)
189 189  # run.to_xarray(daq_map)
190 190  {{/code}}
191 191  
192 -
193 -
194 -{{/expand}}
103 +\\
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