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Wiki source code of DEMO - Working with FLASH data

Last modified by sndueste on 2025-04-23 14:53
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sndueste 42.5 1 Experimental data is recorded as HDF files[[~[link~]>>doc:FS-FLASH USER tmp.Data Acquisition and controls 1.DAQ and controls overview.Offline data analysis (DAQ).The FLASH HDF5 structure.WebHome]] on the GPFS file system[[~[link~]>>https://docs.desy.de/asap3/]]. 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.
cpassow 21.1 2
sndueste 38.1 3 {{info title="How to login JupyterHub"}}
4 === ===
cpassow 26.1 5
sndueste 38.1 6 {{view-file att--filename="tmp.mp4" height="150"/}}
7 {{/info}}
cpassow 26.1 8
sndueste 35.1 9 {{info}}
sndueste 41.1 10 === There are different options that help you to work with the FLASH HDF5 data in Python ===
sndueste 35.1 11
sndueste 39.1 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"]]
sndueste 35.1 14
sndueste 42.4 15 (% class="Object" %)See also the collection of Demo data and sample scripts : [[doc:FS-FLASH USER tmp.Data Acquisition and controls 1.DAQ and controls overview.Offline data analysis (DAQ).Collection of HDF5 sample data from different beamlines.WebHome]]
sndueste 35.1 16 {{/info}}
17
cpassow 26.1 18
sndueste 36.1 19 [[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
sndueste 33.1 20
sndueste 34.1 21 {{expand title="older ideas ..."}}
sndueste 36.1 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"]]
sndueste 33.1 23
cpassow 21.1 24 ----
25
26 === TODO ===
27
cpassow 22.1 28 (% class="task-list" %)
29 (((
30 {{task reference="/Tasks/Task_18" status="InProgress"}}
sndueste 41.3 31 Short descriptions including Links:   → as Text
cpassow 2.1 32
cpassow 22.1 33 (% class="task-list" %)
34 (((
35
36
37 {{task reference="/Tasks/Task_19" status="InProgress"}}
38 GPFS
39 {{/task}}
40
cpassow 27.1 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
sndueste 32.1 53 {{task reference="/Tasks/Task_20" status="InProgress"}}
cpassow 22.1 54 JupyterHub
55 {{/task}}
56
57 {{task reference="/Tasks/Task_21" status="InProgress"}}
58 conda ?
59 {{/task}}
cpassow 23.1 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}}
cpassow 22.1 64 )))
65 {{/task}}
66 )))
67
cpassow 8.1 68
cpassow 22.1 69 (% class="task-list" %)
70 (((
71 {{task reference="/Tasks/Task_22" status="InProgress"}}
72 distribution
cpassow 21.1 73
cpassow 22.1 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
cpassow 21.1 89
cpassow 22.1 90 (% class="task-list" %)
91 (((
92 {{task reference="/Tasks/Task_25" status="InProgress"}}
93 Documentation
cpassow 2.1 94
cpassow 22.1 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
cpassow 2.1 106
cpassow 22.1 107 (% class="task-list" %)
108 (((
109 {{task reference="/Tasks/Task_27" status="InProgress"}}
110 Binder
cpassow 2.1 111
cpassow 22.1 112 (% 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
cpassow 2.1 123
cpassow 22.1 124 (% class="task-list" %)
125 (((
126 {{task reference="/Tasks/Task_29" status="InProgress"}}
127 Screencast
cpassow 15.1 128
cpassow 22.1 129 (% 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
cpassow 2.1 156
cpassow 15.1 157
cpassow 21.1 158 ----
cpassow 2.1 159
cpassow 21.1 160 ==== under review ====
cpassow 4.1 161
162
cpassow 8.1 163 {{code language="bash"}}
cpassow 9.1 164 conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
cpassow 8.1 165 source activate flashh5
cpassow 10.1 166 conda install ipython numpy pandas #TODO: fix dependcies
cpassow 8.1 167 conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
168
169 ## on jhub
cpassow 11.1 170 conda install ipykernel
cpassow 8.1 171 python -m ipykernel install --user --name flashh5 --display-name "flashh5"
172
173
cpassow 11.1 174 ## to remove on jhub
175 ## delete from: /home/$USER/.local/share/jupyter/kernels/
cpassow 8.1 176 {{/code}}
177
sndueste 41.3 178 {{code language="py" title="
179 moved to repository?"}}
cpassow 4.1 180 class RunDirectory:
181
cpassow 21.1 182 def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
cpassow 4.1 183 ...
184
cpassow 21.1 185 def get_run(daq, run_number): # daq is not needed!
186
cpassow 4.1 187 ...
188
189
cpassow 25.1 190 class Run: # constructor optional without RunDirectory or use there self.path
cpassow 4.1 191
cpassow 7.1 192 def get_files():
cpassow 4.1 193 ...
194
cpassow 18.1 195 def get_channels(): # of file #1
cpassow 4.1 196 ...
197
cpassow 8.1 198 def get_start_time(): # better as attribute?
cpassow 4.1 199 ...
200
cpassow 8.1 201 def get_stop_time(): # which? | better as attribute?
cpassow 4.1 202 ...
cpassow 12.1 203
cpassow 19.1 204 def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
cpassow 4.1 205 ...
206
cpassow 7.1 207 def to_series(channel):
cpassow 4.1 208 ...
209
cpassow 7.1 210 def to_array(channel):
cpassow 4.1 211 ...
212 {{/code}}
213
cpassow 6.1 214 {{code language="py" title="ideas"}}
cpassow 10.1 215 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?
cpassow 5.1 218
cpassow 21.1 219 ## interesting?
cpassow 10.1 220 # run.to_dask(daq_map)
221 # run.to_xarray(daq_map)
cpassow 5.1 222 {{/code}}
223
cpassow 30.1 224
sndueste 41.3 225
sndueste 33.1 226 {{/expand}}