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Last modified by makuadm on 2026-01-07 06:21
From version 36.1
edited by sndueste
on 2023-09-29 11:07
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] 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 +(% 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 -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]
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9 +* Links Repository
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11 +** including Method Description
4 4  
5 5  \\
6 6  
7 -{{expand title="How to login JupyterHub"}}
15 +(% style="list-style-type: square;" %)
16 +* Links to Binder
8 8  
9 -
10 -{{view-file att--filename="tmp.mp4" height="250"/}}
11 -{{/expand}}
12 -
13 13  \\
14 14  
15 15  \\
16 16  
17 -{{info}}
18 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
22 +Questions:
19 19  
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}}
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?