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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 3.1
edited by cpassow
on 2022-04-04 08:10
Change comment: There is no comment for this version

Summary

Details

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Title
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1 -DEMO - Working with FLASH data
1 +DEMO - Documentation
Author
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1 -XWiki.sndueste
1 +XWiki.cpassow
Content
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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:
3 +(% style="list-style-type: square;" %)
4 +** GPFS
5 +** JupyterHub
6 +** conda ?
2 2  
3 -\\
8 +(% style="list-style-type: square;" %)
9 +* Links Repository
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11 +** including Method Description
4 4  
5 -{{expand title="How to login JupyterHub"}}
6 -
7 -
8 -{{view-file att--filename="tmp.mp4" height="250"/}}
9 -{{/expand}}
10 -
11 11  \\
12 12  
13 -\\
15 +(% style="list-style-type: square;" %)
16 +* Links to Binder
14 14  
15 -{{info}}
16 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
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
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"]]
21 -{{/info}}
22 -
23 23  \\
24 24  
25 -[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
26 -
27 27  \\
28 28  
29 -{{expand title="older ideas ..."}}
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"]]
22 +Questions:
31 31  
32 -----
33 -
34 -=== TODO ===
35 -
36 -(% class="task-list" %)
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
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 -)))
73 -{{/task}}
74 -)))
75 -
76 -\\
77 -
78 -(% class="task-list" %)
79 -(((
80 -{{task reference="/Tasks/Task_22" status="InProgress"}}
81 -distribution
82 -
83 -(% class="task-list" %)
84 -(((
85 -
86 -
87 -{{task reference="/Tasks/Task_23" status="InProgress"}}
88 -channel  (where to host?)
89 -{{/task}}
90 -
91 -{{task reference="/Tasks/Task_24" status="InProgress"}}
92 -environment file (repository with examples)
93 -{{/task}}
94 -)))
95 -{{/task}}
96 -)))
97 -
98 -\\
99 -
100 -(% class="task-list" %)
101 -(((
102 -{{task reference="/Tasks/Task_25" status="InProgress"}}
103 -Documentation
104 -
105 -(% class="task-list" %)
106 -(((
107 -
108 -
109 -{{task reference="/Tasks/Task_26" status="InProgress"}}
110 -here VS repository VS sphinx
111 -{{/task}}
112 -)))
113 -{{/task}}
114 -)))
115 -
116 -\\
117 -
118 -(% class="task-list" %)
119 -(((
120 -{{task reference="/Tasks/Task_27" status="InProgress"}}
121 -Binder
122 -
123 -(% class="task-list" %)
124 -(((
125 -
126 -
127 -{{task reference="/Tasks/Task_28" status="InProgress"}}
128 -examples with Stefan
129 -{{/task}}
130 -)))
131 -{{/task}}
132 -)))
133 -
134 -\\
135 -
136 -(% class="task-list" %)
137 -(((
138 -{{task reference="/Tasks/Task_29" status="InProgress"}}
139 -Screencast
140 -
141 -(% class="task-list" %)
142 -(((
143 -
144 -
145 -{{task reference="/Tasks/Task_30" status="InProgress"}}
146 -login in jupyter hub
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 -)))
165 -{{/task}}
166 -)))
167 -
168 -\\
169 -
170 -\\
171 -
172 -----
173 -
174 -==== under review ====
175 -
176 -\\
177 -
178 -{{code language="bash"}}
179 -conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
180 -source activate flashh5
181 -conda install ipython numpy pandas #TODO: fix dependcies
182 -conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
183 -
184 -## on jhub
185 -conda install ipykernel
186 -python -m ipykernel install --user --name flashh5 --display-name "flashh5"
187 -
188 -
189 -## to remove on jhub
190 -## delete from: /home/$USER/.local/share/jupyter/kernels/
191 -{{/code}}
192 -
193 -\\
194 -
195 -{{code language="py" title="moved to repository?"}}
196 -class RunDirectory:
197 -
198 - def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
199 - ...
200 -
201 - def get_run(daq, run_number): # daq is not needed!
202 -
203 - ...
204 -
205 -
206 -class Run: # constructor optional without RunDirectory or use there self.path
207 -
208 - def get_files():
209 - ...
210 -
211 - def get_channels(): # of file #1
212 - ...
213 -
214 - def get_start_time(): # better as attribute?
215 - ...
216 -
217 - def get_stop_time(): # which? | better as attribute?
218 - ...
219 -
220 - def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
221 - ...
222 -
223 - def to_series(channel):
224 - ...
225 -
226 - def to_array(channel):
227 - ...
228 -{{/code}}
229 -
230 -{{code language="py" title="ideas"}}
231 -run.to_df(daq_map)
232 -run.to_series(daq_adr or daq_map) # on channel only?
233 -run.to_array(daq_adr) # on channel only?
234 -
235 -## interesting?
236 -# run.to_dask(daq_map)
237 -# run.to_xarray(daq_map)
238 -{{/code}}
239 -
240 -\\
241 -
242 -\\
243 -{{/expand}}
24 +(% style="list-style-type: square;" %)
25 +* for whom
26 +* where Maxwell / local / extern
27 +* distribution\\
28 +(% style="list-style-type: square;" %)
29 +** channel?
30 +(% style="list-style-type: square;" %)
31 +*** where official hosted (DESY, privat, conda-forge)
32 +** enviroment?