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Last modified by makuadm on 2026-01-07 06:21
From version 20.1
edited by cpassow
on 2022-04-04 15:18
Change comment: There is no comment for this version
To version 41.3
edited by sndueste
on 2025-02-05 14:41
Change comment: There is no comment for this version

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Title
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1 -DEMO - Documentation
1 +DEMO - Working with FLASH data
Parent
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1 +FLASHUSER.Data Acquisition and controls.DAQ and controls overview.Offline data analysis (DAQ).WebHome
Author
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1 -XWiki.cpassow
1 +XWiki.sndueste
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1 -(% style="list-style-type: square;" %)
2 -* Short descriptions including Links:   → as Text\\
3 -(% style="list-style-type: square;" %)
4 -** GPFS
5 -** JupyterHub
6 -** conda ?
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.
7 7  
8 -\\
3 +{{info title="How to login JupyterHub"}}
4 +=== ===
9 9  
10 -(% style="list-style-type: square;" %)
11 -* Links Repository
12 -(% style="list-style-type: square;" %)
13 -** including Method Description: Readme or Sphinx ?
6 +{{view-file att--filename="tmp.mp4" height="150"/}}
7 +{{/info}}
14 14  
15 -\\
9 +{{info}}
10 +=== There are different options that help you to work with the FLASH HDF5 data in Python ===
16 16  
17 -(% style="list-style-type: square;" %)
18 -* Links to Binder
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"]]
19 19  
20 -\\
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}}
21 21  
22 -(% style="list-style-type: square;" %)
23 -* Screencast
24 24  
25 -\\
19 +[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
26 26  
27 -\\
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"]]
28 28  
29 -Questions:
24 +----
30 30  
31 -(% style="list-style-type: square;" %)
32 -* distribution\\
33 -(% style="list-style-type: square;" %)
34 -** channel
35 -** enviroment → as example for binder
26 +=== TODO ===
36 36  
37 -\\
28 +(% class="task-list" %)
29 +(((
30 +{{task reference="/Tasks/Task_18" status="InProgress"}}
31 +Short descriptions including Links:   → as Text
38 38  
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 +
39 39  {{code language="bash"}}
40 40  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
41 41  source activate flashh5
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51 51  ## delete from: /home/$USER/.local/share/jupyter/kernels/
52 52  {{/code}}
53 53  
54 -\\
55 -
56 -{{code language="py" title="moved to repository?"}}
178 +{{code language="py" title="
179 +moved to repository?"}}
57 57  class RunDirectory:
58 58  
59 - def get_run_table(): # more or less information? RunComment | Number of Files
182 + def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
60 60   ...
61 61  
62 - def get_run(daq, run_number): # daq is not needed
185 + def get_run(daq, run_number): # daq is not needed!
186 +
63 63   ...
64 64  
65 65  
66 -class Run:
190 +class Run: # constructor optional without RunDirectory or use there self.path
67 67  
68 68   def get_files():
69 69   ...
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76 76  
77 77   def get_stop_time(): # which? | better as attribute?
78 78   ...
79 -
80 -### for following methods to restrict number of files or separate method
81 -### e.g. create_df(files)
82 82  
83 83   def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
84 84   ...
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95 95  run.to_series(daq_adr or daq_map) # on channel only?
96 96  run.to_array(daq_adr) # on channel only?
97 97  
98 -## is this interesting?
219 +## interesting?
99 99  # run.to_dask(daq_map)
100 100  # run.to_xarray(daq_map)
101 101  {{/code}}
102 102  
103 -\\
224 +
225 +
226 +{{/expand}}
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