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Last modified by makuadm on 2026-01-07 06:21
From version 52.1
edited by makuadm
on 2026-01-07 06:21
Change comment: Task [xwiki:FLASHUSER.Offline data analysis (DAQ).DEMO - Working with FLASH data.Tasks.Task_31.WebHome] has been updated!
To version 5.1
edited by cpassow
on 2022-04-04 08:48
Change comment: There is no comment for this version

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Title
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1 -DEMO - Working with FLASH data
1 +DEMO - Documentation
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1 -FLASHUSER.Offline data analysis (DAQ).WebHome
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1 -XWiki.makuadm
1 +XWiki.cpassow
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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.
1 +(% style="list-style-type: square;" %)
2 +* Short descriptions including Links:
3 +(% style="list-style-type: square;" %)
4 +** GPFS
5 +** JupyterHub
6 +** conda ?
2 2  
3 -{{info title="How to login JupyterHub"}}
4 -=== ===
8 +(% style="list-style-type: square;" %)
9 +* Links Repository
10 +(% style="list-style-type: square;" %)
11 +** including Method Description
5 5  
6 -{{view-file att--filename="tmp.mp4" height="150"/}}
7 -{{/info}}
13 +\\
8 8  
9 -{{info}}
10 -=== There are different options that help you to work with the FLASH HDF5 data in Python ===
15 +(% style="list-style-type: square;" %)
16 +* Links to Binder
11 11  
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"]]
18 +\\
14 14  
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}}
20 +\\
17 17  
22 +Questions:
18 18  
19 -[[~[~[image:attach:image2023-9-29_11-1-37.png~]~]>>url:https://hasfcpkg.desy.de/fab/fab.html||shape="rect"]]
24 +(% style="list-style-type: square;" %)
25 +* for whom
26 +* where Maxwell / local / extern
27 +* distribution\\
28 +(% style="list-style-type: square;" %)
29 +** channel?
30 +(% style="list-style-type: square;" %)
31 +*** where official hosted (DESY, privat, conda-forge)
32 +** enviroment?
33 +(% style="list-style-type: square;" %)
34 +*** via files / already created?
20 20  
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"]]
36 +\\
23 23  
24 -----
25 -
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" completeDate="" createDate="2026-01-07" reporter=""}}
40 -distribution
41 -\\
42 -{{/task}}
43 -)))
44 -
45 -
46 -(% class="task-list" %)
47 -(((
48 -{{task reference="/Tasks/Task_25" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
49 -Documentation
50 -\\
51 -{{/task}}
52 -)))
53 -
54 -
55 -(% class="task-list" %)
56 -(((
57 -{{task reference="/Tasks/Task_27" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
58 -Binder
59 -\\
60 -{{/task}}
61 -)))
62 -
63 -
64 -(% class="task-list" %)
65 -(((
66 -{{task reference="/Tasks/Task_29" status="InProgress" completeDate="" createDate="2026-01-07" reporter=""}}
67 -Screencast
68 -\\
69 -{{/task}}
70 -)))
71 -
72 -
73 -
74 -----
75 -
76 -==== under review ====
77 -
78 -
79 -{{code language="bash"}}
80 -conda create -n flashh5 python=3.10 # 3.10 not necessary, but would prefer 3.8 or higher
81 -source activate flashh5
82 -conda install ipython numpy pandas #TODO: fix dependcies
83 -conda install -c https://www.desy.de/~cpassow/condarepo/ flashh5
84 -
85 -## on jhub
86 -conda install ipykernel
87 -python -m ipykernel install --user --name flashh5 --display-name "flashh5"
88 -
89 -
90 -## to remove on jhub
91 -## delete from: /home/$USER/.local/share/jupyter/kernels/
92 -{{/code}}
93 -
94 -{{code language="py" title="
95 -moved to repository?"}}
38 +{{code language="py"}}
96 96  class RunDirectory:
97 97  
98 - def get_run_table(): # more or less information? RunComment | Number of Files | start & stop time ?
41 + def get_run_table(self):
99 99   ...
100 100  
101 - def get_run(daq, run_number): # daq is not needed!
102 -
44 + def get_run(self, daq, run_number):
103 103   ...
104 104  
105 105  
106 -class Run: # constructor optional without RunDirectory or use there self.path
48 +class Run:
107 107  
108 - def get_files():
50 + def get_files(self):
109 109   ...
110 110  
111 - def get_channels(): # of file #1
53 + def get_channels(self): # of file #1?
112 112   ...
113 113  
114 - def get_start_time(): # better as attribute?
56 + def get_start_time(self):
115 115   ...
116 116  
117 - def get_stop_time(): # which? | better as attribute?
59 + def get_stop_time(self): # which?
118 118   ...
119 -
120 - def to_df(daq_map): # to_df(daq_map, slice) slice=[0:4] -> throw Exception
61 +
62 + def to_df(self, channel_dict):
121 121   ...
122 122  
123 - def to_series(channel):
65 + def to_series(self, channel):
124 124   ...
125 125  
126 - def to_array(channel):
68 + def to_array(self, channel):
127 127   ...
128 128  {{/code}}
129 129  
130 -{{code language="py" title="ideas"}}
131 -run.to_df(daq_map)
132 -run.to_series(daq_adr or daq_map) # on channel only?
133 -run.to_array(daq_adr) # on channel only?
72 +{{code language="py"}}
73 +run.to_df(channel_dict)
74 +run.to_series(channel_string or channel_dict) # on channel only?
75 +run.to_array(channel_string) # on channel only?
134 134  
135 -## interesting?
136 -# run.to_dask(daq_map)
137 -# run.to_xarray(daq_map)
77 +# run.to_dask(dict)
78 +# run.to_xarray(dict)
138 138  {{/code}}
139 139  
140 -
141 -
142 -{{/expand}}
81 +\\
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