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Last modified by makuadm on 2026-01-07 06:21
From version 41.3
edited by sndueste
on 2025-02-05 14:41
Change comment: There is no comment for this version
To version 1.1
edited by cpassow
on 2022-03-31 11:41
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 -FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).WebHome
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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.DAQ and controls overview.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.
2 -
3 -{{info title="How to login JupyterHub"}}
4 -=== ===
5 -
6 -{{view-file att--filename="tmp.mp4" height="150"/}}
7 -{{/info}}
8 -
9 -{{info}}
10 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
11 -
12 -* The currently developed option for large data sets: [[the FAB package>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]] ... see below
13 -* 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"]]
14 -
15 -(% 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]]
16 -{{/info}}
17 -
18 -
19 -[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
20 -
21 -{{expand title="older ideas ..."}}
22 -(% class="Object" %)(object oriented) [[https:~~/~~/gitlab.desy.de/christopher.passow/fdh-builder>>url:https://gitlab.desy.de/christopher.passow/fdh-builder.git||shape="rect"]]
23 -
24 -----
25 -
26 -=== TODO ===
27 -
28 -(% class="task-list" %)
29 -(((
30 -{{task reference="/Tasks/Task_18" status="InProgress"}}
31 -Short descriptions including Links:   → as Text
32 -
33 -(% class="task-list" %)
34 -(((
35 -
36 -
37 -{{task reference="/Tasks/Task_19" status="InProgress"}}
38 -GPFS
39 -{{/task}}
40 -
41 -{{task reference="/Tasks/Task_40" status="InProgress"}}
42 -Access rights
43 -{{/task}}
44 -
45 -{{task reference="/Tasks/Task_41" status="InProgress"}}
46 -Gamma Portal
47 -{{/task}}
48 -
49 -{{task reference="/Tasks/Task_42" status="InProgress"}}
50 -Maxwell
51 -{{/task}}
52 -
53 -{{task reference="/Tasks/Task_20" status="InProgress"}}
54 -JupyterHub
55 -{{/task}}
56 -
57 -{{task reference="/Tasks/Task_21" status="InProgress"}}
58 -conda ?
59 -{{/task}}
60 -
61 -{{task reference="/Tasks/Task_36" status="InProgress"}}
62 -explain install from channel instead of fixed environment, but can use environment file from example repository
63 -{{/task}}
64 -)))
65 -{{/task}}
66 -)))
67 -
68 -
69 -(% class="task-list" %)
70 -(((
71 -{{task reference="/Tasks/Task_22" status="InProgress"}}
72 -distribution
73 -
74 -(% class="task-list" %)
75 -(((
76 -
77 -
78 -{{task reference="/Tasks/Task_23" status="InProgress"}}
79 -channel  (where to host?)
80 -{{/task}}
81 -
82 -{{task reference="/Tasks/Task_24" status="InProgress"}}
83 -environment file (repository with examples)
84 -{{/task}}
85 -)))
86 -{{/task}}
87 -)))
88 -
89 -
90 -(% class="task-list" %)
91 -(((
92 -{{task reference="/Tasks/Task_25" status="InProgress"}}
93 -Documentation
94 -
95 -(% class="task-list" %)
96 -(((
97 -
98 -
99 -{{task reference="/Tasks/Task_26" status="InProgress"}}
100 -here VS repository VS sphinx
101 -{{/task}}
102 -)))
103 -{{/task}}
104 -)))
105 -
106 -
107 -(% class="task-list" %)
108 -(((
109 -{{task reference="/Tasks/Task_27" status="InProgress"}}
110 -Binder
111 -
112 -(% class="task-list" %)
113 -(((
114 -
115 -
116 -{{task reference="/Tasks/Task_28" status="InProgress"}}
117 -examples with Stefan
118 -{{/task}}
119 -)))
120 -{{/task}}
121 -)))
122 -
123 -
124 -(% class="task-list" %)
125 -(((
126 -{{task reference="/Tasks/Task_29" status="InProgress"}}
127 -Screencast
128 -
129 -(% class="task-list" %)
130 -(((
131 -
132 -
133 -{{task reference="/Tasks/Task_30" status="InProgress"}}
134 -login in jupyter hub
135 -{{/task}}
136 -
137 -{{task reference="/Tasks/Task_31" status="InProgress"}}
138 -login maxwell display
139 -{{/task}}
140 -
141 -{{task reference="/Tasks/Task_32" status="InProgress"}}
142 -use slix
143 -{{/task}}
144 -
145 -{{task reference="/Tasks/Task_33" status="InProgress"}}
146 -use hdfview plugin in jupterLab
147 -{{/task}}
148 -
149 -{{task reference="/Tasks/Task_34" status="InProgress"}}
150 -create conda env with flashh5
151 -{{/task}}
152 -)))
153 -{{/task}}
154 -)))
155 -
156 -
157 -
158 -----
159 -
160 -==== under review ====
161 -
162 -
163 -{{code language="bash"}}
164 -conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
165 -source activate flashh5
166 -conda install ipython numpy pandas #TODO: fix dependcies
167 -conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
168 -
169 -## on jhub
170 -conda install ipykernel
171 -python -m ipykernel install --user --name flashh5 --display-name "flashh5"
172 -
173 -
174 -## to remove on jhub
175 -## delete from: /home/$USER/.local/share/jupyter/kernels/
176 -{{/code}}
177 -
178 -{{code language="py" title="
179 -moved to repository?"}}
180 -class RunDirectory:
181 -
182 - def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
183 - ...
184 -
185 - def get_run(daq, run_number): # daq is not needed!
186 -
187 - ...
188 -
189 -
190 -class Run: # constructor optional without RunDirectory or use there self.path
191 -
192 - def get_files():
193 - ...
194 -
195 - def get_channels(): # of file #1
196 - ...
197 -
198 - def get_start_time(): # better as attribute?
199 - ...
200 -
201 - def get_stop_time(): # which? | better as attribute?
202 - ...
203 -
204 - def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
205 - ...
206 -
207 - def to_series(channel):
208 - ...
209 -
210 - def to_array(channel):
211 - ...
212 -{{/code}}
213 -
214 -{{code language="py" title="ideas"}}
215 -run.to_df(daq_map)
216 -run.to_series(daq_adr or daq_map) # on channel only?
217 -run.to_array(daq_adr) # on channel only?
218 -
219 -## interesting?
220 -# run.to_dask(daq_map)
221 -# run.to_xarray(daq_map)
222 -{{/code}}
223 -
224 -
225 -
226 -{{/expand}}
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