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Last modified by makuadm on 2026-01-07 06:21
From version 19.1
edited by cpassow
on 2022-04-04 11:58
Change comment: There is no comment for this version
To version 41.1
edited by sndueste
on 2025-02-05 11:21
Change comment: Renamed back-links.

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Title
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1 -DEMO - Documentation
1 +DEMO - Working with FLASH data
Author
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1 -XWiki.cpassow
1 +XWiki.sndueste
Content
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1 -(% style="list-style-type: square;" %)
2 -* Short descriptions including Links:
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.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.
7 7  
3 +{{info title="How to login JupyterHub"}}
4 +=== ===
5 +
6 +{{view-file att--filename="tmp.mp4" height="150"/}}
7 +{{/info}}
8 +
8 8  \\
9 9  
10 -(% style="list-style-type: square;" %)
11 -* Links Repository
12 -(% style="list-style-type: square;" %)
13 -** including Method Description?
11 +{{info}}
12 +=== There are different options that help you to work with the FLASH HDF5 data in Python ===
14 14  
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.DAQ and controls overview.Offline data analysis (DAQ).Collection of HDF5 sample data from different beamlines.WebHome]]
18 +{{/info}}
19 +
15 15  \\
16 16  
17 -(% style="list-style-type: square;" %)
18 -* Links to Binder
22 +[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
19 19  
20 20  \\
21 21  
22 -(% style="list-style-type: square;" %)
23 -* Screencast
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"]]
24 24  
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 +
25 25  \\
26 26  
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 +
27 27  \\
28 28  
29 -Questions:
97 +(% class="task-list" %)
98 +(((
99 +{{task reference="/Tasks/Task_25" status="InProgress"}}
100 +Documentation
30 30  
31 -(% style="list-style-type: square;" %)
32 -* for whom
33 -* where Maxwell / local / extern
34 -* distribution\\
35 -(% style="list-style-type: square;" %)
36 -** channel?
37 -(% style="list-style-type: square;" %)
38 -*** where official hosted (DESY, privat, conda-forge)
39 -** enviroment?
40 -(% style="list-style-type: square;" %)
41 -*** via files / already created?
102 +(% class="task-list" %)
103 +(((
104 +
42 42  
106 +{{task reference="/Tasks/Task_26" status="InProgress"}}
107 +here VS repository VS sphinx
108 +{{/task}}
109 +)))
110 +{{/task}}
111 +)))
112 +
43 43  \\
44 44  
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 +
45 45  {{code language="bash"}}
46 46  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
47 47  source activate flashh5
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62 62  {{code language="py" title="moved to repository?"}}
63 63  class RunDirectory:
64 64  
65 - def get_run_table(): # more or less information? RunComment | Number of Files
195 + def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
66 66   ...
67 67  
68 - def get_run(daq, run_number): # daq is not needed
198 + def get_run(daq, run_number): # daq is not needed!
199 +
69 69   ...
70 70  
71 71  
72 -class Run:
203 +class Run: # constructor optional without RunDirectory or use there self.path
73 73  
74 74   def get_files():
75 75   ...
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82 82  
83 83   def get_stop_time(): # which? | better as attribute?
84 84   ...
85 -
86 -### for following methods to restrict number of files or separate method
87 -### e.g. create_df(files)
88 88  
89 89   def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
90 90   ...
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101 101  run.to_series(daq_adr or daq_map) # on channel only?
102 102  run.to_array(daq_adr) # on channel only?
103 103  
104 -## is this interesting?
232 +## interesting?
105 105  # run.to_dask(daq_map)
106 106  # run.to_xarray(daq_map)
107 107  {{/code}}
108 108  
109 109  \\
238 +
239 +\\
240 +{{/expand}}
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