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Last modified by makuadm on 2026-01-07 06:21
From version 41.1
edited by sndueste
on 2025-02-05 11:21
Change comment: Renamed back-links.
To version 20.1
edited by cpassow
on 2022-04-04 15:18
Change comment: There is no comment for this version

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1 -DEMO - Working with FLASH data
1 +DEMO - Documentation
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1 -XWiki.sndueste
1 +XWiki.cpassow
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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 +(% 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 -=== ===
5 -
6 -{{view-file att--filename="tmp.mp4" height="150"/}}
7 -{{/info}}
8 -
9 9  \\
10 10  
11 -{{info}}
12 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
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11 +* Links Repository
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13 +** including Method Description: Readme or Sphinx ?
13 13  
14 -* The currently developed option for large data sets: [[the FAB package>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]] ... see below
15 -* 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"]]
16 -
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]]
18 -{{/info}}
19 -
20 20  \\
21 21  
22 -[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
17 +(% style="list-style-type: square;" %)
18 +* Links to Binder
23 23  
24 24  \\
25 25  
26 -{{expand title="older ideas ..."}}
27 -(% 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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23 +* Screencast
28 28  
29 -----
30 -
31 -=== TODO ===
32 -
33 -(% class="task-list" %)
34 -(((
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
44 -{{/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}}
69 -)))
70 -{{/task}}
71 -)))
72 -
73 73  \\
74 74  
75 -(% class="task-list" %)
76 -(((
77 -{{task reference="/Tasks/Task_22" status="InProgress"}}
78 -distribution
79 -
80 -(% class="task-list" %)
81 -(((
82 -
83 -
84 -{{task reference="/Tasks/Task_23" status="InProgress"}}
85 -channel  (where to host?)
86 -{{/task}}
87 -
88 -{{task reference="/Tasks/Task_24" status="InProgress"}}
89 -environment file (repository with examples)
90 -{{/task}}
91 -)))
92 -{{/task}}
93 -)))
94 -
95 95  \\
96 96  
97 -(% class="task-list" %)
98 -(((
99 -{{task reference="/Tasks/Task_25" status="InProgress"}}
100 -Documentation
29 +Questions:
101 101  
102 -(% class="task-list" %)
103 -(((
104 -
31 +(% style="list-style-type: square;" %)
32 +* distribution\\
33 +(% style="list-style-type: square;" %)
34 +** channel
35 +** enviroment → as example for binder
105 105  
106 -{{task reference="/Tasks/Task_26" status="InProgress"}}
107 -here VS repository VS sphinx
108 -{{/task}}
109 -)))
110 -{{/task}}
111 -)))
112 -
113 113  \\
114 114  
115 -(% class="task-list" %)
116 -(((
117 -{{task reference="/Tasks/Task_27" status="InProgress"}}
118 -Binder
119 -
120 -(% class="task-list" %)
121 -(((
122 -
123 -
124 -{{task reference="/Tasks/Task_28" status="InProgress"}}
125 -examples with Stefan
126 -{{/task}}
127 -)))
128 -{{/task}}
129 -)))
130 -
131 -\\
132 -
133 -(% class="task-list" %)
134 -(((
135 -{{task reference="/Tasks/Task_29" status="InProgress"}}
136 -Screencast
137 -
138 -(% class="task-list" %)
139 -(((
140 -
141 -
142 -{{task reference="/Tasks/Task_30" status="InProgress"}}
143 -login in jupyter hub
144 -{{/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}}
161 -)))
162 -{{/task}}
163 -)))
164 -
165 -\\
166 -
167 -\\
168 -
169 -----
170 -
171 -==== under review ====
172 -
173 -\\
174 -
175 175  {{code language="bash"}}
176 176  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
177 177  source activate flashh5
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192 192  {{code language="py" title="moved to repository?"}}
193 193  class RunDirectory:
194 194  
195 - 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
196 196   ...
197 197  
198 - def get_run(daq, run_number): # daq is not needed!
199 -
62 + def get_run(daq, run_number): # daq is not needed
200 200   ...
201 201  
202 202  
203 -class Run: # constructor optional without RunDirectory or use there self.path
66 +class Run:
204 204  
205 205   def get_files():
206 206   ...
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213 213  
214 214   def get_stop_time(): # which? | better as attribute?
215 215   ...
79 +
80 +### for following methods to restrict number of files or separate method
81 +### e.g. create_df(files)
216 216  
217 217   def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
218 218   ...
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229 229  run.to_series(daq_adr or daq_map) # on channel only?
230 230  run.to_array(daq_adr) # on channel only?
231 231  
232 -## interesting?
98 +## is this interesting?
233 233  # run.to_dask(daq_map)
234 234  # run.to_xarray(daq_map)
235 235  {{/code}}
236 236  
237 237  \\
238 -
239 -\\
240 -{{/expand}}
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