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Last modified by flenners on 2026-02-04 17:25
From version 13.1
edited by flenners
on 2024-05-24 14:55
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To version 5.1
edited by flenners
on 2022-09-16 09:16
Change comment: There is no comment for this version

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1 -== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 -
3 -Terminal:
4 -
5 -\\
6 -
7 -salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
8 -\\(if you need gpu: ~-~-constraint=P100 )
9 -
10 -//Answer~:// salloc: job [//number//] queued and waiting for resources
11 -
12 - salloc: job [number] has been allocated resources
13 -
14 - salloc: Granted job allocation [number]
15 -
16 - salloc: Waiting for resource configuration
17 -
18 - 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)
19 -
20 -(% class="code" %)
21 -(((
22 -ssh max-wn035 (shell to your node)
23 -\\module load maxwell mamba
24 -)))
25 -
26 -(% class="code" %)
27 -(((
28 -
29 -. mamba-init (. is important! never do without, this can crash your FastX)
30 -\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
31 -)))
32 -
33 -
34 -spyder &
35 -\\~-~-~-~-~-~-
36 -\\\\Spyder will open.
37 -
38 -On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
39 -
40 -[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
41 -
42 -\\
43 -
44 -Important: you need to be in the right folder, else the script will not be able to find a file in the first cell of the script
45 -
46 -\\
47 -
48 -Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
49 -
50 -\\
51 -
52 -\\
53 -
54 54  = {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
55 55  \\ =
56 56  
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72 72  
73 73  **HOLOTOMO DATA**
74 74  
75 -Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
22 +Hint: you have to perform the phase reconstruction of your projections first!
76 76  
77 77  Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
78 78  
79 79  The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
80 80  
81 -Click on one file and click open
82 -
83 83  You do not need to load any additional dark images.
84 84  
85 85  Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
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90 90  
91 91  = {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
92 92  
93 -(Can be skipped for Holotomography)
38 +\\
94 94  
95 95  Go to "Prep" tab.
96 96  
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130 130  
131 131  **Finding the correct center of rotation. **
132 132  
133 -First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation
78 +First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation.
134 134  
135 -**~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.)
80 +**Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
136 136  
137 -**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. 
82 +**Delta:** Range which is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
138 138  
139 -**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)
84 +**Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center.
140 140  
141 -**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.)
86 +Slice: Slice which will be reconstructed. You can also check different slices for checking the rotation center.
142 142  
143 -**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.
144 -
145 -[[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
146 -
147 -in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
148 -
149 -**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.
150 -
151 151  \\
152 152  
153 -How does a good rotation center look like?
154 -
155 -(% class="relative-table wrapped" style="width: 57.8179%;" %)
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157 -good
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184 -[[image:attach:image2022-11-14_15-7-13.png||height="250"]]
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187 -The ghosting effect on the edges is due to sample movement during the scan.
188 -)))
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204 -**[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
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210 -[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
211 -
212 -\\
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214 -\\
215 -
216 216  **Reconstruction Parameters. **
217 217  
218 218  When you found the correct rotation center, you can continue with the reconstruction.
219 219  
220 -Enter the final roation center from the above step.
94 +Enter the final roation center from the above step.
221 221  
222 222  You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
223 223  
Confluence.Code.ConfluencePageClass[0]
Id
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1 -365845773
1 +275770572
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/365845773/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/275770572/03a Reconstruction with Reco GUI