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Last modified by flenners on 2026-02-04 17:25
From version 16.1
edited by greving
on 2024-12-12 18:06
Change comment: There is no comment for this version
To version 19.2
edited by flenners
on 2026-02-04 17:24
Change comment: There is no comment for this version

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1 -XWiki.greving
1 +XWiki.flenners
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1 1  == {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 2  
3 -Terminal:
4 4  
4 +Open the following link in a browser and log in with your DESY account (not door account!).
5 5  
6 -salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
7 -\\(if you need gpu: ~-~-partition=psxgpu )
6 +[[https:~~/~~/max-display.desy.de:3389/auth/ssh>>url:https://max-display.desy.de:3443/auth/ssh]]
8 8  
8 +Start a new XFCE session by clicking on the running mouse:, select browser session
9 +
10 +[[image:image2021-4-27_13-55-52.png||height="405" width="911"]]
11 +
12 +
13 +Open a terminal:
14 +
15 +[[image:1770222205178-264.png]]
16 +
17 +In this terminal, type:
18 +
19 +{{{salloc --partition=psxcpu --nodes=1 --time=06:00:00}}}
20 +
21 +(((
22 +
23 +)))
24 +
25 +(((
26 +(if you need gpu: ~-~-partition=psxgpu )
27 +)))
28 +
29 +(((
9 9  //Answer~:// salloc: job [//number//] queued and waiting for resources
31 +)))
10 10  
33 +(((
11 11   salloc: job [number] has been allocated resources
35 +)))
12 12  
37 +(((
13 13   salloc: Granted job allocation [number]
39 +)))
14 14  
41 +(((
15 15   salloc: Waiting for resource configuration
43 +)))
16 16  
45 +(((
17 17   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)
47 +)))
18 18  
19 19  (% class="code" %)
20 20  (((
51 +(((
21 21  ssh max-wn035 (shell to your node)
22 22  \\module load maxwell mamba
23 23  )))
55 +)))
24 24  
25 25  (% class="code" %)
26 26  (((
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68 68  
69 69  Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
70 70  
71 -Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
103 +Go to "Load" tab, load processed data.
72 72  
73 -The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
105 +Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
74 74  
75 -Click on one file and click open
107 +Click on "Load processed"
76 76  
77 77  You do not need to load any additional dark images.
78 78  
79 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
111 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg. padding are still optional. (see below)
80 80  
81 81  In principle, you can directly proceed to the third tab "Reconstruction". 
82 82  
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102 102  
103 103  **Binning:** You can bin your data before reconstruction. Since the detector has a point spread function of 2-3 pixels, it is save to bin by a factor of 2 without loosing spatial resolution. This reduces computation time and storage space needed.
104 104  
105 -**Padding:** If your samples are significantly __larger__ than the field of view, you can pad your data to prevent artifacts at the outer field of view. Example: 100
137 +**Padding:** **//RECOMENDED FOR ROI scans//**! If your samples are significantly __larger__ than the field of view, you can pad your data to prevent artifacts at the outer field of view. Example: 100
106 106  
107 107  **Filter Projections before reconstruction:** You can filter the data before reconstruction. This reduces the noise, but also can induce blurring in the data. Only recommended for very noisy data. Filtering after reconstruction is usually better.
108 108  
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