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

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.flenners
1 +XWiki.greving
Content
... ... @@ -1,58 +1,26 @@
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 -
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 -(((
30 30  //Answer~:// salloc: job [//number//] queued and waiting for resources
31 -)))
32 32  
33 -(((
34 34   salloc: job [number] has been allocated resources
35 -)))
36 36  
37 -(((
38 38   salloc: Granted job allocation [number]
39 -)))
40 40  
41 -(((
42 42   salloc: Waiting for resource configuration
43 -)))
44 44  
45 -(((
46 46   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 -)))
48 48  
49 49  (% class="code" %)
50 50  (((
51 -(((
52 52  ssh max-wn035 (shell to your node)
53 53  \\module load maxwell mamba
54 54  )))
55 -)))
56 56  
57 57  (% class="code" %)
58 58  (((
... ... @@ -100,15 +100,15 @@
100 100  
101 101  Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
102 102  
103 -Go to "Load" tab, load processed data.
71 +Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
104 104  
105 -Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
73 +The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
106 106  
107 -Click on "Load processed"
75 +Click on one file and click open
108 108  
109 109  You do not need to load any additional dark images.
110 110  
111 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg. padding are still optional. (see below)
79 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
112 112  
113 113  In principle, you can directly proceed to the third tab "Reconstruction". 
114 114  
... ... @@ -134,7 +134,7 @@
134 134  
135 135  **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.
136 136  
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
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
138 138  
139 139  **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.
140 140  
1770222205178-264.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.flenners
Size
... ... @@ -1,1 +1,0 @@
1 -218.5 KB
Content
image2021-4-27_13-55-52.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.flenners
Size
... ... @@ -1,1 +1,0 @@
1 -92.4 KB
Content