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Last modified by makuadm on 2026-01-07 06:21
From version 40.1
edited by sndueste
on 2023-11-01 16:52
Change comment: There is no comment for this version
To version 2.1
edited by cpassow
on 2022-04-04 08:06
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.
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2 +* Short descriptions including Links:
3 +(% style="list-style-type: square;" %)
4 +** GPFS
5 +** JupyterHub
6 +** conda ?
2 2  
3 -{{info title="How to login JupyterHub"}}
4 -=== ===
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9 +* Links Repository
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11 +** including Method Description
5 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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16 +* Links to Binder
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.Data Access at FLASH (DAQ, gpfs,\.\.\.).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"]]
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"]]
22 +Questions:
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 -\\
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 -\\
96 -
97 -(% class="task-list" %)
98 -(((
99 -{{task reference="/Tasks/Task_25" status="InProgress"}}
100 -Documentation
101 -
102 -(% class="task-list" %)
103 -(((
104 -
105 -
106 -{{task reference="/Tasks/Task_26" status="InProgress"}}
107 -here VS repository VS sphinx
108 -{{/task}}
109 -)))
110 -{{/task}}
111 -)))
112 -
113 -\\
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 -{{code language="bash"}}
176 -conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
177 -source activate flashh5
178 -conda install ipython numpy pandas #TODO: fix dependcies
179 -conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
180 -
181 -## on jhub
182 -conda install ipykernel
183 -python -m ipykernel install --user --name flashh5 --display-name "flashh5"
184 -
185 -
186 -## to remove on jhub
187 -## delete from: /home/$USER/.local/share/jupyter/kernels/
188 -{{/code}}
189 -
190 -\\
191 -
192 -{{code language="py" title="moved to repository?"}}
193 -class RunDirectory:
194 -
195 - def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
196 - ...
197 -
198 - def get_run(daq, run_number): # daq is not needed!
199 -
200 - ...
201 -
202 -
203 -class Run: # constructor optional without RunDirectory or use there self.path
204 -
205 - def get_files():
206 - ...
207 -
208 - def get_channels(): # of file #1
209 - ...
210 -
211 - def get_start_time(): # better as attribute?
212 - ...
213 -
214 - def get_stop_time(): # which? | better as attribute?
215 - ...
216 -
217 - def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
218 - ...
219 -
220 - def to_series(channel):
221 - ...
222 -
223 - def to_array(channel):
224 - ...
225 -{{/code}}
226 -
227 -{{code language="py" title="ideas"}}
228 -run.to_df(daq_map)
229 -run.to_series(daq_adr or daq_map) # on channel only?
230 -run.to_array(daq_adr) # on channel only?
231 -
232 -## interesting?
233 -# run.to_dask(daq_map)
234 -# run.to_xarray(daq_map)
235 -{{/code}}
236 -
237 -\\
238 -
239 -\\
240 -{{/expand}}
24 +(% style="list-style-type: square;" %)
25 +* for whom
26 +* where Maxwell / local / extern
27 +* distribution
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