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Last modified by flenners on 2026-02-04 17:25
From version 9.1
edited by wirtenss
on 2022-11-29 10:25
Change comment: There is no comment for this version
To version 14.1
edited by flenners
on 2024-06-25 11:43
Change comment: There is no comment for this version

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1 -XWiki.wirtenss
1 +XWiki.flenners
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1 +== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 +
3 +Terminal:
4 +
5 +\\
6 +
7 +salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
8 +\\(if you need gpu: ~-~-constraint=P100 )
9 +
10 +//Answer~:// salloc: job [//number//] queued and waiting for resources
11 +
12 + salloc: job [number] has been allocated resources
13 +
14 + salloc: Granted job allocation [number]
15 +
16 + salloc: Waiting for resource configuration
17 +
18 + salloc: Nodes //max-wn035// are ready for job  (name of your node; code after “max-“ can vary, in this example wn035, if you do not get a specific node name, repeat salloc command)
19 +
20 +(% class="code" %)
21 +(((
22 +ssh max-wn035 (shell to your node)
23 +\\module load maxwell mamba
24 +)))
25 +
26 +(% class="code" %)
27 +(((
28 +
29 +. mamba-init (. is important! never do without, this can crash your FastX)
30 +\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
31 +)))
32 +
33 +
34 +spyder &
35 +\\~-~-~-~-~-~-
36 +\\\\Spyder will open.
37 +
38 +On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
39 +
40 +[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
41 +
42 +\\
43 +
44 +Important: you need to be in the right folder, else the script will not be able to find a file in the first cell of the script
45 +
46 +\\
47 +
48 +Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
49 +
50 +\\
51 +
52 +\\
53 +
1 1  = {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
2 2  \\ =
3 3  
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19 19  
20 20  **HOLOTOMO DATA**
21 21  
22 -Hint: you have to perform the phase reconstruction of your projections first!
75 +Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
23 23  
24 24  Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
25 25  
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99 99  
100 100  How does a good rotation center look like?
101 101  
102 -(% class="relative-table wrapped" style="width: 57.8179%;" %)
155 +(% class="relative-table wrapped" style="width: 37.5112%;" %)
103 103  |=(((
104 104  good
105 105  )))|=(((
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134 134  The ghosting effect on the edges is due to sample movement during the scan.
135 135  )))
136 136  |(((
190 +\\
191 +)))|(((
192 +\\
193 +)))|(((
194 +\\
195 +)))
196 +|(((
137 137  (% class="content-wrapper" %)
138 138  (((
139 139  [[image:attach:image2022-11-14_15-29-47.png||height="250"]]
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147 147  \\
148 148  )))
149 149  
150 -\\
210 +[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
151 151  
152 152  \\
153 153  
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -293405975
1 +236814957
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/293405975/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/236814957/03a Reconstruction with Reco GUI