Skip to Content
Last modified by flenners on 2026-02-04 17:25
From version 15.1
edited by greving
on 2024-12-12 18:05
Change comment: There is no comment for this version
To version 20.1
edited by flenners
on 2026-02-04 17:25
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.greving
1 +XWiki.flenners
Content
... ... @@ -1,26 +1,63 @@
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  (((
... ... @@ -28,11 +28,13 @@
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"]]
... ... @@ -45,9 +45,10 @@
45 45  
46 46  
47 47  
48 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
49 - =
87 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
50 50  
89 += =
90 +
51 51  **TXM DATA**
52 52  
53 53  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -67,15 +67,15 @@
67 67  
68 68  Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
69 69  
70 -Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
110 +Go to "Load" tab, load processed data.
71 71  
72 -The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
112 +Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
73 73  
74 -Click on one file and click open
114 +Click on "Load processed"
75 75  
76 76  You do not need to load any additional dark images.
77 77  
78 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps 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)
79 79  
80 80  In principle, you can directly proceed to the third tab "Reconstruction". 
81 81  
... ... @@ -82,7 +82,7 @@
82 82  
83 83  = {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
84 84  
85 -(Can be skipped for Holotomography)
125 +(**Can be skipped for Holotomography**)
86 86  
87 87  Go to "Prep" tab.
88 88  
... ... @@ -101,7 +101,7 @@
101 101  
102 102  **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.
103 103  
104 -**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
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
105 105  
106 106  **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.
107 107  
1770222205178-264.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.flenners
Size
... ... @@ -1,0 +1,1 @@
1 +218.5 KB
Content
image2021-4-27_13-55-52.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.flenners
Size
... ... @@ -1,0 +1,1 @@
1 +92.4 KB
Content