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Last modified by flenners on 2026-02-04 17:25
From version 16.2
edited by flenners
on 2026-02-04 17:15
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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 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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72 72  
73 73  Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
74 74  
75 -Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
107 +Click on "Load processed"
76 76  
77 -
78 78  You do not need to load any additional dark images.
79 79  
80 -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)
81 81  
82 82  In principle, you can directly proceed to the third tab "Reconstruction". 
83 83  
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103 103  
104 104  **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.
105 105  
106 -**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
107 107  
108 108  **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.
109 109  
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