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Last modified by flenners on 2026-02-04 17:25
From version 14.1
edited by flenners
on 2024-06-25 11:43
Change comment: There is no comment for this version
To version 7.1
edited by wirtenss
on 2022-11-14 14:12
Change comment: Anleitung fürs Rotationszentrum erweitert

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1 -XWiki.flenners
1 +XWiki.wirtenss
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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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150 150  
151 151  \\
152 152  
153 -How does a good rotation center look like?
154 -
155 -(% class="relative-table wrapped" style="width: 37.5112%;" %)
156 -|=(((
157 -good
158 -)))|=(((
159 -bad
160 -)))|=(((
161 -comment
162 -)))
163 -|(((
164 -(% class="content-wrapper" %)
165 -(((
166 -[[image:attach:image2022-11-14_14-17-45.png||height="250"]]
167 -)))
168 -)))|(((
169 -(% class="content-wrapper" %)
170 -(((
171 -[[image:attach:image2022-11-14_14-19-33.png||height="250"]]
172 -)))
173 -)))|(((
174 174  \\
175 -)))
176 -|(((
177 -(% class="content-wrapper" %)
178 -(((
179 -[[image:attach:image2022-11-14_15-16-34.png||height="250"]]
180 -)))
181 -)))|(((
182 -(% class="content-wrapper" %)
183 -(((
184 -[[image:attach:image2022-11-14_15-7-13.png||height="250"]]
185 -)))
186 -)))|(((
187 -The ghosting effect on the edges is due to sample movement during the scan.
188 -)))
189 -|(((
190 -\\
191 -)))|(((
192 -\\
193 -)))|(((
194 -\\
195 -)))
196 -|(((
197 -(% class="content-wrapper" %)
198 -(((
199 -[[image:attach:image2022-11-14_15-29-47.png||height="250"]]
200 -)))
201 -)))|(((
202 -(% class="content-wrapper" %)
203 -(((
204 -**[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
205 -)))
206 -)))|(((
207 -\\
208 -)))
209 209  
210 -[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
211 -
212 212  \\
213 213  
214 -\\
215 -
216 216  **Reconstruction Parameters. **
217 217  
218 218  When you found the correct rotation center, you can continue with the reconstruction.
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1 -236814957
1 +284692086
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/236814957/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/284692086/03a Reconstruction with Reco GUI