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Last modified by flenners on 2026-02-04 17:25
From version 12.1
edited by flenners
on 2024-05-24 14:52
Change comment: There is no comment for this version
To version 16.1
edited by greving
on 2024-12-12 18:06
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-LoadingData"/}}Loading Data
2 -\\ =
1 +== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
3 3  
3 +Terminal:
4 +
5 +
6 +salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
7 +\\(if you need gpu: ~-~-partition=psxgpu )
8 +
9 +//Answer~:// salloc: job [//number//] queued and waiting for resources
10 +
11 + salloc: job [number] has been allocated resources
12 +
13 + salloc: Granted job allocation [number]
14 +
15 + salloc: Waiting for resource configuration
16 +
17 + 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)
18 +
19 +(% class="code" %)
20 +(((
21 +ssh max-wn035 (shell to your node)
22 +\\module load maxwell mamba
23 +)))
24 +
25 +(% class="code" %)
26 +(((
27 +. mamba-init (. is important! never do without, this can crash your FastX)
28 +\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
29 +)))
30 +
31 +
32 +spyder &
33 +\\~-~-~-~-~-~-
34 +\\\\Spyder will open.
35 +
36 +On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
37 +
38 +[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
39 +
40 +
41 +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
42 +
43 +
44 +Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
45 +
46 +
47 +
48 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
49 +
50 += =
51 +
4 4  **TXM DATA**
5 5  
6 6  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
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15 15  
16 16  Continue with next step, "Preparation".
17 17  
18 -\\
19 19  
20 20  **HOLOTOMO DATA**
21 21  
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33 33  
34 34  In principle, you can directly proceed to the third tab "Reconstruction". 
35 35  
36 -\\
37 37  
38 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
84 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
39 39  
40 -(Can be skipped for Holotomography)
86 +(**Can be skipped for Holotomography**)
41 41  
42 42  Go to "Prep" tab.
43 43  
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49 49  
50 50  Click "Rotate" button.
51 51  
52 -\\
53 53  
54 54  The following steps are **optional:**
55 55  
56 -**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.
101 +**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.
57 57  
58 58  **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.
59 59  
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61 61  
62 62  **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.
63 63  
64 -\\
65 65  
66 66  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
67 67  
68 -\\
69 69  
70 70  **Save current stack.** Writes the normalized projections to your beamtime folder.
71 71  
72 -\\
73 73  
74 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
116 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
75 75  
76 -\\
77 77  
78 78  **Finding the correct center of rotation. **
79 79  
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95 95  
96 96  **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.
97 97  
98 -\\
99 99  
100 100  How does a good rotation center look like?
101 101  
102 -(% class="relative-table wrapped" style="width: 57.8179%;" %)
142 +(% class="relative-table wrapped" style="width:37.5112%" %)
103 103  |=(((
104 104  good
105 105  )))|=(((
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118 118  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
119 119  )))
120 120  )))|(((
121 -\\
161 +
122 122  )))
123 123  |(((
124 124  (% class="content-wrapper" %)
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134 134  The ghosting effect on the edges is due to sample movement during the scan.
135 135  )))
136 136  |(((
137 -\\
177 +
138 138  )))|(((
139 -\\
179 +
140 140  )))|(((
141 -\\
181 +
142 142  )))
143 143  |(((
144 144  (% class="content-wrapper" %)
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151 151  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
152 152  )))
153 153  )))|(((
154 -\\
194 +
155 155  )))
156 156  
157 157  [[image:attach:image2023-1-23_11-39-57.png||height="400"]]
158 158  
159 -\\
160 160  
161 -\\
162 162  
163 163  **Reconstruction Parameters. **
164 164  
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174 174  
175 175  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".
176 176  
177 -\\
178 178  
179 179  When you are happy with your result, press "Reconstruct full stack".
180 180  
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182 182  
183 183  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.
184 184  
185 -\\
186 186  
187 -\\
188 188  
189 -\\
190 190  
191 -\\
225 +
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -361457350
1 +236814957
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/361457350/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/236814957/03a Reconstruction with Reco GUI