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Last modified by flenners on 2026-02-04 17:25
From version 17.2
edited by flenners
on 2026-02-04 17:19
Change comment: There is no comment for this version
To version 15.1
edited by greving
on 2024-12-12 18:05
Change comment: There is no comment for this version

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1 -XWiki.flenners
1 +XWiki.greving
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1 1  == {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 2  
3 -
4 -Open the following link in a browser and log in with your DESY account (not door account!).
5 -
6 -[[https:~~/~~/max-display.desy.de:3389/auth/ssh>>url:https://max-display.desy.de:3443/auth/ssh]]
7 -
8 -Start a 
9 -
10 -
11 -
12 12  Terminal:
13 13  
14 14  
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54 54  
55 55  
56 56  
57 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
48 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
49 + =
58 58  
59 -= =
60 -
61 61  **TXM DATA**
62 62  
63 63  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
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77 77  
78 78  Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
79 79  
80 -Go to "Load" tab, load processed data.
70 +Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
81 81  
82 -Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
72 +The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
83 83  
84 -Click on "Load processed"
74 +Click on one file and click open
85 85  
86 86  You do not need to load any additional dark images.
87 87  
88 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg. padding are still optional. (see below)
78 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
89 89  
90 90  In principle, you can directly proceed to the third tab "Reconstruction". 
91 91  
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92 92  
93 93  = {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
94 94  
95 -(**Can be skipped for Holotomography**)
85 +(Can be skipped for Holotomography)
96 96  
97 97  Go to "Prep" tab.
98 98  
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111 111  
112 112  **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.
113 113  
114 -**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
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
115 115  
116 116  **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.
117 117