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Last modified by flenners on 2026-02-04 17:25
From version 20.1
edited by flenners
on 2026-02-04 17:25
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To version 16.2
edited by flenners
on 2026-02-04 17:15
Change comment: There is no comment for this version

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1 1  == {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 2  
3 +Terminal:
3 3  
4 -Open the following link in a browser and log in with your DESY account (not door account!).
5 5  
6 -[[https:~~/~~/max-display.desy.de:3389/auth/ssh>>url:https://max-display.desy.de:3443/auth/ssh]]
6 +salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
7 +\\(if you need gpu: ~-~-partition=psxgpu )
7 7  
8 -Start a new XFCE session by clicking on the running mouse:, select browser session
9 +//Answer~:// salloc: job [//number//] queued and waiting for resources
9 9  
10 -[[image:image2021-4-27_13-55-52.png||height="405" width="911"]]
11 + salloc: job [number] has been allocated resources
11 11  
13 + salloc: Granted job allocation [number]
12 12  
13 -Open a terminal:
15 + salloc: Waiting for resource configuration
14 14  
15 -[[image:1770222205178-264.png]]
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)
16 16  
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 -
50 50  (% class="code" %)
51 51  (((
52 -(((
53 -
54 -)))
55 -
56 -(((
57 57  ssh max-wn035 (shell to your node)
58 58  \\module load maxwell mamba
59 59  )))
60 -)))
61 61  
62 62  (% class="code" %)
63 63  (((
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65 65  \\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
66 66  )))
67 67  
68 -{{{spyder &
69 69  
70 -------
32 +spyder &
33 +\\~-~-~-~-~-~-
34 +\\\\Spyder will open.
71 71  
72 -
73 -Spyder will open. }}}
74 -
75 75  On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
76 76  
77 77  [[image:attach:image2022-11-1_13-7-14.png||height="250"]]
... ... @@ -111,11 +111,12 @@
111 111  
112 112  Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
113 113  
114 -Click on "Load processed"
75 +Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
115 115  
77 +
116 116  You do not need to load any additional dark images.
117 117  
118 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg. padding are still optional. (see below)
80 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
119 119  
120 120  In principle, you can directly proceed to the third tab "Reconstruction". 
121 121  
... ... @@ -141,7 +141,7 @@
141 141  
142 142  **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.
143 143  
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 +**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
145 145  
146 146  **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.
147 147  
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