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Wiki source code of DEMO - Working with FLASH data

Version 45.1 by makuadm on 2026-01-06 21:19
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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"}}
makuadm 43.1 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 (((
makuadm 43.1 30 {{task reference="/Tasks/Task_18" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
sndueste 41.3 31 Short descriptions including Links:   → as Text
makuadm 43.1 32 \\
cpassow 22.1 33 {{/task}}
34 )))
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cpassow 8.1 36
cpassow 22.1 37 (% class="task-list" %)
38 (((
39 {{task reference="/Tasks/Task_22" status="InProgress"}}
40 distribution
cpassow 21.1 41
cpassow 22.1 42 (% class="task-list" %)
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46 {{task reference="/Tasks/Task_23" status="InProgress"}}
47 channel  (where to host?)
48 {{/task}}
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50 {{task reference="/Tasks/Task_24" status="InProgress"}}
51 environment file (repository with examples)
52 {{/task}}
53 )))
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55 )))
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cpassow 21.1 57
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59 (((
60 {{task reference="/Tasks/Task_25" status="InProgress"}}
61 Documentation
cpassow 2.1 62
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67 {{task reference="/Tasks/Task_26" status="InProgress"}}
68 here VS repository VS sphinx
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cpassow 2.1 74
cpassow 22.1 75 (% class="task-list" %)
76 (((
77 {{task reference="/Tasks/Task_27" status="InProgress"}}
78 Binder
cpassow 2.1 79
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84 {{task reference="/Tasks/Task_28" status="InProgress"}}
85 examples with Stefan
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cpassow 2.1 91
cpassow 22.1 92 (% class="task-list" %)
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94 {{task reference="/Tasks/Task_29" status="InProgress"}}
95 Screencast
cpassow 15.1 96
cpassow 22.1 97 (% class="task-list" %)
98 (((
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101 {{task reference="/Tasks/Task_30" status="InProgress"}}
102 login in jupyter hub
103 {{/task}}
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105 {{task reference="/Tasks/Task_31" status="InProgress"}}
106 login maxwell display
107 {{/task}}
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109 {{task reference="/Tasks/Task_32" status="InProgress"}}
110 use slix
111 {{/task}}
112
makuadm 44.1 113 {{task reference="/Tasks/Task_33" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
cpassow 22.1 114 use hdfview plugin in jupterLab
115 {{/task}}
116
makuadm 45.1 117 {{task reference="/Tasks/Task_34" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
cpassow 22.1 118 create conda env with flashh5
119 {{/task}}
120 )))
121 {{/task}}
122 )))
123
cpassow 2.1 124
cpassow 15.1 125
cpassow 21.1 126 ----
cpassow 2.1 127
cpassow 21.1 128 ==== under review ====
cpassow 4.1 129
130
cpassow 8.1 131 {{code language="bash"}}
cpassow 9.1 132 conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
cpassow 8.1 133 source activate flashh5
cpassow 10.1 134 conda install ipython numpy pandas #TODO: fix dependcies
cpassow 8.1 135 conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
136
137 ## on jhub
cpassow 11.1 138 conda install ipykernel
cpassow 8.1 139 python -m ipykernel install --user --name flashh5 --display-name "flashh5"
140
141
cpassow 11.1 142 ## to remove on jhub
143 ## delete from: /home/$USER/.local/share/jupyter/kernels/
cpassow 8.1 144 {{/code}}
145
sndueste 41.3 146 {{code language="py" title="
147 moved to repository?"}}
cpassow 4.1 148 class RunDirectory:
149
cpassow 21.1 150 def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
cpassow 4.1 151 ...
152
cpassow 21.1 153 def get_run(daq, run_number): # daq is not needed!
154
cpassow 4.1 155 ...
156
157
cpassow 25.1 158 class Run: # constructor optional without RunDirectory or use there self.path
cpassow 4.1 159
cpassow 7.1 160 def get_files():
cpassow 4.1 161 ...
162
cpassow 18.1 163 def get_channels(): # of file #1
cpassow 4.1 164 ...
165
cpassow 8.1 166 def get_start_time(): # better as attribute?
cpassow 4.1 167 ...
168
cpassow 8.1 169 def get_stop_time(): # which? | better as attribute?
cpassow 4.1 170 ...
cpassow 12.1 171
cpassow 19.1 172 def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
cpassow 4.1 173 ...
174
cpassow 7.1 175 def to_series(channel):
cpassow 4.1 176 ...
177
cpassow 7.1 178 def to_array(channel):
cpassow 4.1 179 ...
180 {{/code}}
181
cpassow 6.1 182 {{code language="py" title="ideas"}}
cpassow 10.1 183 run.to_df(daq_map)
184 run.to_series(daq_adr or daq_map) # on channel only?
185 run.to_array(daq_adr) # on channel only?
cpassow 5.1 186
cpassow 21.1 187 ## interesting?
cpassow 10.1 188 # run.to_dask(daq_map)
189 # run.to_xarray(daq_map)
cpassow 5.1 190 {{/code}}
191
cpassow 30.1 192
sndueste 41.3 193
sndueste 33.1 194 {{/expand}}