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Last modified by flenners on 2026-02-04 17:25
From version 11.1
edited by flenners
on 2023-11-27 14:35
Change comment: There is no comment for this version
To version 13.1
edited by flenners
on 2024-05-24 14:55
Change comment: There is no comment for this version

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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  
Confluence.Code.ConfluencePageClass[0]
Id
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1 -361457340
1 +365845773
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/361457340/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/365845773/03a Reconstruction with Reco GUI