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Last modified by makuadm on 2026-01-07 06:21
From version 2.1
edited by cpassow
on 2022-04-04 08:06
Change comment: There is no comment for this version
To version 36.1
edited by sndueste
on 2023-09-29 11:07
Change comment: There is no comment for this version

Summary

Details

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Title
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1 -DEMO - Documentation
1 +DEMO - Working with FLASH data
Author
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1 -XWiki.cpassow
1 +XWiki.sndueste
Content
... ... @@ -1,27 +1,245 @@
1 -(% style="list-style-type: square;" %)
2 -* Short descriptions including Links:
3 -(% style="list-style-type: square;" %)
4 -** GPFS
5 -** JupyterHub
6 -** conda ?
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.
7 7  
8 -(% style="list-style-type: square;" %)
9 -* Links Repository
10 -(% style="list-style-type: square;" %)
11 -** including Method Description
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]
12 12  
13 13  \\
14 14  
15 -(% style="list-style-type: square;" %)
16 -* Links to Binder
7 +{{expand title="How to login JupyterHub"}}
17 17  
9 +
10 +{{view-file att--filename="tmp.mp4" height="250"/}}
11 +{{/expand}}
12 +
18 18  \\
19 19  
20 20  \\
21 21  
22 -Questions:
17 +{{info}}
18 +=== There are different options that help you to work with the FLASH HDF5 data in Python ===
23 23  
24 -(% style="list-style-type: square;" %)
25 -* for whom
26 -* where Maxwell / local / extern
27 -* distribution
20 +The currently developed option for large data sets: [[the FAB package>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]] ... see below
21 +
22 +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"]]
23 +{{/info}}
24 +
25 +\\
26 +
27 +[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
28 +
29 +\\
30 +
31 +{{expand title="older ideas ..."}}
32 +(% class="Object" %)(object oriented) [[https:~~/~~/gitlab.desy.de/christopher.passow/fdh-builder>>url:https://gitlab.desy.de/christopher.passow/fdh-builder.git||shape="rect"]]
33 +
34 +----
35 +
36 +=== TODO ===
37 +
38 +(% class="task-list" %)
39 +(((
40 +{{task reference="/Tasks/Task_18" status="InProgress"}}
41 +Short descriptions including Links:   → as Text\\
42 +
43 +(% class="task-list" %)
44 +(((
45 +
46 +
47 +{{task reference="/Tasks/Task_19" status="InProgress"}}
48 +GPFS
49 +{{/task}}
50 +
51 +{{task reference="/Tasks/Task_40" status="InProgress"}}
52 +Access rights
53 +{{/task}}
54 +
55 +{{task reference="/Tasks/Task_41" status="InProgress"}}
56 +Gamma Portal
57 +{{/task}}
58 +
59 +{{task reference="/Tasks/Task_42" status="InProgress"}}
60 +Maxwell
61 +{{/task}}
62 +
63 +{{task reference="/Tasks/Task_20" status="InProgress"}}
64 +JupyterHub
65 +{{/task}}
66 +
67 +{{task reference="/Tasks/Task_21" status="InProgress"}}
68 +conda ?
69 +{{/task}}
70 +
71 +{{task reference="/Tasks/Task_36" status="InProgress"}}
72 +explain install from channel instead of fixed environment, but can use environment file from example repository
73 +{{/task}}
74 +)))
75 +{{/task}}
76 +)))
77 +
78 +\\
79 +
80 +(% class="task-list" %)
81 +(((
82 +{{task reference="/Tasks/Task_22" status="InProgress"}}
83 +distribution
84 +
85 +(% class="task-list" %)
86 +(((
87 +
88 +
89 +{{task reference="/Tasks/Task_23" status="InProgress"}}
90 +channel  (where to host?)
91 +{{/task}}
92 +
93 +{{task reference="/Tasks/Task_24" status="InProgress"}}
94 +environment file (repository with examples)
95 +{{/task}}
96 +)))
97 +{{/task}}
98 +)))
99 +
100 +\\
101 +
102 +(% class="task-list" %)
103 +(((
104 +{{task reference="/Tasks/Task_25" status="InProgress"}}
105 +Documentation
106 +
107 +(% class="task-list" %)
108 +(((
109 +
110 +
111 +{{task reference="/Tasks/Task_26" status="InProgress"}}
112 +here VS repository VS sphinx
113 +{{/task}}
114 +)))
115 +{{/task}}
116 +)))
117 +
118 +\\
119 +
120 +(% class="task-list" %)
121 +(((
122 +{{task reference="/Tasks/Task_27" status="InProgress"}}
123 +Binder
124 +
125 +(% class="task-list" %)
126 +(((
127 +
128 +
129 +{{task reference="/Tasks/Task_28" status="InProgress"}}
130 +examples with Stefan
131 +{{/task}}
132 +)))
133 +{{/task}}
134 +)))
135 +
136 +\\
137 +
138 +(% class="task-list" %)
139 +(((
140 +{{task reference="/Tasks/Task_29" status="InProgress"}}
141 +Screencast
142 +
143 +(% class="task-list" %)
144 +(((
145 +
146 +
147 +{{task reference="/Tasks/Task_30" status="InProgress"}}
148 +login in jupyter hub
149 +{{/task}}
150 +
151 +{{task reference="/Tasks/Task_31" status="InProgress"}}
152 +login maxwell display
153 +{{/task}}
154 +
155 +{{task reference="/Tasks/Task_32" status="InProgress"}}
156 +use slix
157 +{{/task}}
158 +
159 +{{task reference="/Tasks/Task_33" status="InProgress"}}
160 +use hdfview plugin in jupterLab
161 +{{/task}}
162 +
163 +{{task reference="/Tasks/Task_34" status="InProgress"}}
164 +create conda env with flashh5
165 +{{/task}}
166 +)))
167 +{{/task}}
168 +)))
169 +
170 +\\
171 +
172 +\\
173 +
174 +----
175 +
176 +==== under review ====
177 +
178 +\\
179 +
180 +{{code language="bash"}}
181 +conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
182 +source activate flashh5
183 +conda install ipython numpy pandas #TODO: fix dependcies
184 +conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
185 +
186 +## on jhub
187 +conda install ipykernel
188 +python -m ipykernel install --user --name flashh5 --display-name "flashh5"
189 +
190 +
191 +## to remove on jhub
192 +## delete from: /home/$USER/.local/share/jupyter/kernels/
193 +{{/code}}
194 +
195 +\\
196 +
197 +{{code language="py" title="moved to repository?"}}
198 +class RunDirectory:
199 +
200 + def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
201 + ...
202 +
203 + def get_run(daq, run_number): # daq is not needed!
204 +
205 + ...
206 +
207 +
208 +class Run: # constructor optional without RunDirectory or use there self.path
209 +
210 + def get_files():
211 + ...
212 +
213 + def get_channels(): # of file #1
214 + ...
215 +
216 + def get_start_time(): # better as attribute?
217 + ...
218 +
219 + def get_stop_time(): # which? | better as attribute?
220 + ...
221 +
222 + def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
223 + ...
224 +
225 + def to_series(channel):
226 + ...
227 +
228 + def to_array(channel):
229 + ...
230 +{{/code}}
231 +
232 +{{code language="py" title="ideas"}}
233 +run.to_df(daq_map)
234 +run.to_series(daq_adr or daq_map) # on channel only?
235 +run.to_array(daq_adr) # on channel only?
236 +
237 +## interesting?
238 +# run.to_dask(daq_map)
239 +# run.to_xarray(daq_map)
240 +{{/code}}
241 +
242 +\\
243 +
244 +\\
245 +{{/expand}}