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Last modified by flenners on 2026-02-04 17:25
From version 16.3
edited by flenners
on 2026-02-04 17:16
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To version 20.1
edited by flenners
on 2026-02-04 17:25
Change comment: There is no comment for this version

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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  
9 -//Answer~:// salloc: job [//number//] queued and waiting for resources
8 +Start a new XFCE session by clicking on the running mouse:, select browser session
10 10  
11 - salloc: job [number] has been allocated resources
10 +[[image:image2021-4-27_13-55-52.png||height="405" width="911"]]
12 12  
13 - salloc: Granted job allocation [number]
14 14  
15 - salloc: Waiting for resource configuration
13 +Open a terminal:
16 16  
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)
15 +[[image:1770222205178-264.png]]
18 18  
17 +
18 +In this terminal, type:
19 +
20 +{{{salloc --partition=psxcpu --nodes=1 --time=06:00:00}}}
21 +
22 +(((
23 +
24 +)))
25 +
26 +(((
27 +//(if you need gpu: ~-~-partition=psxgpu )//
28 +)))
29 +
30 +(((
31 +//Answer: salloc: job [number] queued and waiting for resources//
32 +)))
33 +
34 +(((
35 +// salloc: job [number] has been allocated resources//
36 +)))
37 +
38 +(((
39 +// salloc: Granted job allocation [number]//
40 +)))
41 +
42 +(((
43 +// salloc: Waiting for resource configuration//
44 +)))
45 +
46 +(((
47 +// 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)//
48 +)))
49 +
19 19  (% class="code" %)
20 20  (((
52 +(((
53 +
54 +)))
55 +
56 +(((
21 21  ssh max-wn035 (shell to your node)
22 22  \\module load maxwell mamba
23 23  )))
60 +)))
24 24  
25 25  (% class="code" %)
26 26  (((
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28 28  \\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
29 29  )))
30 30  
68 +{{{spyder &
31 31  
32 -spyder &
33 -\\~-~-~-~-~-~-
34 -\\\\Spyder will open.
70 +------
35 35  
72 +
73 +Spyder will open. }}}
74 +
36 36  On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
37 37  
38 38  [[image:attach:image2022-11-1_13-7-14.png||height="250"]]
... ... @@ -76,7 +76,7 @@
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, eg.  are still optional. (see below)
118 +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:** 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
144 +**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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