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Last modified by makuadm on 2026-01-07 06:21
From version 9.1
edited by cpassow
on 2022-04-04 09:31
Change comment: There is no comment for this version
To version 43.1
edited by makuadm
on 2026-01-06 20:39
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_18.WebHome] has been updated!

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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.Offline data analysis (DAQ).WebHome
Author
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1 -XWiki.cpassow
1 +XWiki.makuadm
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: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.
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?
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: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]]
16 +{{/info}}
21 21  
22 -\\
23 23  
24 -Questions:
19 +[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
25 25  
26 -(% style="list-style-type: square;" %)
27 -* for whom
28 -* where Maxwell / local / extern
29 -* distribution\\
30 -(% style="list-style-type: square;" %)
31 -** channel?
32 -(% style="list-style-type: square;" %)
33 -*** where official hosted (DESY, privat, conda-forge)
34 -** enviroment?
35 -(% style="list-style-type: square;" %)
36 -*** via files / already created?
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"]]
37 37  
38 -\\
24 +----
39 39  
26 +=== TODO ===
27 +
28 +(% class="task-list" %)
29 +(((
30 +{{task reference="/Tasks/Task_18" status="InProgress" completeDate="" createDate="2026-01-06" reporter=""}}
31 +Short descriptions including Links:   → as Text
32 +\\
33 +{{/task}}
34 +)))
35 +
36 +
37 +(% class="task-list" %)
38 +(((
39 +{{task reference="/Tasks/Task_22" status="InProgress"}}
40 +distribution
41 +
42 +(% class="task-list" %)
43 +(((
44 +
45 +
46 +{{task reference="/Tasks/Task_23" status="InProgress"}}
47 +channel  (where to host?)
48 +{{/task}}
49 +
50 +{{task reference="/Tasks/Task_24" status="InProgress"}}
51 +environment file (repository with examples)
52 +{{/task}}
53 +)))
54 +{{/task}}
55 +)))
56 +
57 +
58 +(% class="task-list" %)
59 +(((
60 +{{task reference="/Tasks/Task_25" status="InProgress"}}
61 +Documentation
62 +
63 +(% class="task-list" %)
64 +(((
65 +
66 +
67 +{{task reference="/Tasks/Task_26" status="InProgress"}}
68 +here VS repository VS sphinx
69 +{{/task}}
70 +)))
71 +{{/task}}
72 +)))
73 +
74 +
75 +(% class="task-list" %)
76 +(((
77 +{{task reference="/Tasks/Task_27" status="InProgress"}}
78 +Binder
79 +
80 +(% class="task-list" %)
81 +(((
82 +
83 +
84 +{{task reference="/Tasks/Task_28" status="InProgress"}}
85 +examples with Stefan
86 +{{/task}}
87 +)))
88 +{{/task}}
89 +)))
90 +
91 +
92 +(% class="task-list" %)
93 +(((
94 +{{task reference="/Tasks/Task_29" status="InProgress"}}
95 +Screencast
96 +
97 +(% class="task-list" %)
98 +(((
99 +
100 +
101 +{{task reference="/Tasks/Task_30" status="InProgress"}}
102 +login in jupyter hub
103 +{{/task}}
104 +
105 +{{task reference="/Tasks/Task_31" status="InProgress"}}
106 +login maxwell display
107 +{{/task}}
108 +
109 +{{task reference="/Tasks/Task_32" status="InProgress"}}
110 +use slix
111 +{{/task}}
112 +
113 +{{task reference="/Tasks/Task_33" status="InProgress"}}
114 +use hdfview plugin in jupterLab
115 +{{/task}}
116 +
117 +{{task reference="/Tasks/Task_34" status="InProgress"}}
118 +create conda env with flashh5
119 +{{/task}}
120 +)))
121 +{{/task}}
122 +)))
123 +
124 +
125 +
126 +----
127 +
128 +==== under review ====
129 +
130 +
40 40  {{code language="bash"}}
41 41  conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
42 42  source activate flashh5
43 -conda install ipython numpy pandas # fix dependcies
134 +conda install ipython numpy pandas #TODO: fix dependcies
44 44  conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
45 45  
46 46  ## on jhub
138 +conda install ipykernel
47 47  python -m ipykernel install --user --name flashh5 --display-name "flashh5"
48 48  
49 49  
142 +## to remove on jhub
143 +## delete from: /home/$USER/.local/share/jupyter/kernels/
50 50  {{/code}}
51 51  
52 -\\
53 -
54 -\\
55 -
56 -{{code language="py" title="moved to repository?"}}
146 +{{code language="py" title="
147 +moved to repository?"}}
57 57  class RunDirectory:
58 58  
59 - def get_run_table():
150 + 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):
153 + def get_run(daq, run_number): # daq is not needed!
154 +
63 63   ...
64 64  
65 65  
66 -class Run:
158 +class Run: # constructor optional without RunDirectory or use there self.path
67 67  
68 68   def get_files():
69 69   ...
70 70  
71 - def get_channels(): # of file #1?
163 + def get_channels(): # of file #1
72 72   ...
73 73  
74 74   def get_start_time(): # better as attribute?
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76 76  
77 77   def get_stop_time(): # which? | better as attribute?
78 78   ...
79 -
80 - def to_df(channel_map):
171 +
172 + def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
81 81   ...
82 82  
83 83   def to_series(channel):
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88 88  {{/code}}
89 89  
90 90  {{code language="py" title="ideas"}}
91 -run.to_df(channel_map)
92 -run.to_series(channel_string or channel_map) # on channel only?
93 -run.to_array(channel_string) # on channel only?
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?
94 94  
95 -## is this interesting?
96 -# run.to_dask(dict)
97 -# run.to_xarray(dict)
187 +## interesting?
188 +# run.to_dask(daq_map)
189 +# run.to_xarray(daq_map)
98 98  {{/code}}
99 99  
100 -\\
192 +
193 +
194 +{{/expand}}
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