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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
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 -== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
1 +== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 2  
3 3  Terminal:
4 4  
5 -\\
6 6  
7 -salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
8 -\\(if you need gpu: ~-~-constraint=P100 )
6 +salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
7 +\\(if you need gpu: ~-~-partition=psxgpu )
9 9  
10 10  //Answer~:// salloc: job [//number//] queued and waiting for resources
11 11  
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25 25  
26 26  (% class="code" %)
27 27  (((
28 -
29 29  . mamba-init (. is important! never do without, this can crash your FastX)
30 30  \\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
31 31  )))
32 32  
33 33  
34 -spyder &
32 +spyder &
35 35  \\~-~-~-~-~-~-
36 36  \\\\Spyder will open.
37 37  
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39 39  
40 40  [[image:attach:image2022-11-1_13-7-14.png||height="250"]]
41 41  
42 -\\
43 43  
44 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 45  
46 -\\
47 47  
48 48  Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
49 49  
50 -\\
51 51  
52 -\\
53 53  
54 54  = {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
55 -\\ =
49 + =
56 56  
57 57  **TXM DATA**
58 58  
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68 68  
69 69  Continue with next step, "Preparation".
70 70  
71 -\\
72 72  
73 73  **HOLOTOMO DATA**
74 74  
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86 86  
87 87  In principle, you can directly proceed to the third tab "Reconstruction". 
88 88  
89 -\\
90 90  
91 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
83 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
92 92  
93 93  (Can be skipped for Holotomography)
94 94  
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102 102  
103 103  Click "Rotate" button.
104 104  
105 -\\
106 106  
107 107  The following steps are **optional:**
108 108  
109 -**Cropping:** If your samples are significantly (% style="color: rgb(0,51,102);" %)__smaller__(%%) than the field of view, you can crop the data to reduce computation time and storage. Draw a rectangle around your sample by keeping the left mouse button pressed. Check that your sample stays inside that rectangle at all angles. If you are happy, press the "crop" button to crop your data.
100 +**Cropping:** If your samples are significantly (% style="color:#003366" %)__smaller__(%%) than the field of view, you can crop the data to reduce computation time and storage. Draw a rectangle around your sample by keeping the left mouse button pressed. Check that your sample stays inside that rectangle at all angles. If you are happy, press the "crop" button to crop your data.
110 110  
111 111  **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.
112 112  
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114 114  
115 115  **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.
116 116  
117 -\\
118 118  
119 119  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
120 120  
121 -\\
122 122  
123 123  **Save current stack.** Writes the normalized projections to your beamtime folder.
124 124  
125 -\\
126 126  
127 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
115 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
128 128  
129 -\\
130 130  
131 131  **Finding the correct center of rotation. **
132 132  
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148 148  
149 149  **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.
150 150  
151 -\\
152 152  
153 153  How does a good rotation center look like?
154 154  
155 -(% class="relative-table wrapped" style="width: 57.8179%;" %)
141 +(% class="relative-table wrapped" style="width:37.5112%" %)
156 156  |=(((
157 157  good
158 158  )))|=(((
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171 171  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
172 172  )))
173 173  )))|(((
174 -\\
160 +
175 175  )))
176 176  |(((
177 177  (% class="content-wrapper" %)
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187 187  The ghosting effect on the edges is due to sample movement during the scan.
188 188  )))
189 189  |(((
190 -\\
176 +
191 191  )))|(((
192 -\\
178 +
193 193  )))|(((
194 -\\
180 +
195 195  )))
196 196  |(((
197 197  (% class="content-wrapper" %)
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204 204  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
205 205  )))
206 206  )))|(((
207 -\\
193 +
208 208  )))
209 209  
210 210  [[image:attach:image2023-1-23_11-39-57.png||height="400"]]
211 211  
212 -\\
213 213  
214 -\\
215 215  
216 216  **Reconstruction Parameters. **
217 217  
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227 227  
228 228  before the final reconstruction, you can reconstruct a test slice to check your reconstruction parameters. Enter the slice number you want to reconstruct and press " Reconstruct slice".
229 229  
230 -\\
231 231  
232 232  When you are happy with your result, press "Reconstruct full stack".
233 233  
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235 235  
236 236  When you are finished with one scan, please press the "clear all" button! This saves the log data you see on the right, so you can later check what you did. The data are also removed from the memory.
237 237  
238 -\\
239 239  
240 -\\
241 241  
242 -\\
243 243  
244 -\\
224 +
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Confluence.Code.ConfluencePageClass[0]
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1 -365845773
1 +236814957
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/236814957/03a Reconstruction with Reco GUI