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Last modified by flenners on 2026-02-04 17:25
From version 7.1
edited by wirtenss
on 2022-11-14 14:12
Change comment: Anleitung fürs Rotationszentrum erweitert
To version 4.1
edited by flenners
on 2021-12-17 14:14
Change comment: There is no comment for this version

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1 -XWiki.wirtenss
1 +XWiki.flenners
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19 19  
20 20  **HOLOTOMO DATA**
21 21  
22 -Hint: you have to perform the phase reconstruction of your projections first!
22 +We are still in "friendly user operation" for this mode and the reconstruction pipeline is still work in progress.
23 23  
24 -Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
24 +Update soon ...
25 25  
26 -The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
26 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
27 27  
28 -You do not need to load any additional dark images.
29 -
30 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
31 -
32 -In principle, you can directly proceed to the third tab "Reconstruction". 
33 -
34 34  \\
35 35  
36 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
37 -
38 -(Can be skipped for Holotomography)
39 -
40 40  Go to "Prep" tab.
41 41  
42 42  The following is usually required for reconstruction:
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75 75  
76 76  **Finding the correct center of rotation. **
77 77  
78 -First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation
68 +First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation.
79 79  
80 -**~1. Rot center: **Defines the rotation center in pixel coordinates. For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
70 +**Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
81 81  
82 -**2. Delta: **Range of pixels around the in step 1 given rot center for which the test slice is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
72 +**Delta:** Range which is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
83 83  
84 -**3. Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center. (for example [ ... , 507, 512, 517, ... ] for a stepsize of 5)
74 +**Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center.
85 85  
86 -**4. Slice:** Defines the pixel row which is used to reconstruct the test slice. Tip: Choose a region where you expect to see distinctive structures. (You can also check different slices for checking the rotation center.)
76 +Slice: Slice which will be reconstructed. You can also check different slices for checking the rotation center.
87 87  
88 -**5. Check rotation center: **Click on the "Check rotation center" button.** **In the preview window move the slider around until you find the positions with the least artifacts. Remember the position number and check the Spyder Console to get the new rot center coordinates in pixel.
89 -
90 -[[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
91 -
92 -in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
93 -
94 -**6. Update and Repeat:** Replace the Rot Center (step 1) with the new found coordinate, lower the Delta (step 2) and Stepsize (step 3) and repeat the process until you are satisfied with the result.
95 -
96 96  \\
97 97  
98 -\\
99 -
100 -\\
101 -
102 102  **Reconstruction Parameters. **
103 103  
104 104  When you found the correct rotation center, you can continue with the reconstruction.
105 105  
106 -Enter the final roation center from the above step.
84 +Enter the final roation center from the above step.
107 107  
108 108  You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
109 109  
Confluence.Code.ConfluencePageClass[0]
Id
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1 -284692086
1 +275758009
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/284692086/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/275758009/03a Reconstruction with Reco GUI