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Last modified by flenners on 2026-02-04 17:25
From version 16.3
edited by flenners
on 2026-02-04 17:16
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To version 13.1
edited by flenners
on 2024-05-24 14:55
Change comment: There is no comment for this version

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1 -== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
1 +== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 2  
3 3  Terminal:
4 4  
5 +\\
5 5  
6 -salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
7 -\\(if you need gpu: ~-~-partition=psxgpu )
7 +salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
8 +\\(if you need gpu: ~-~-constraint=P100 )
8 8  
9 9  //Answer~:// salloc: job [//number//] queued and waiting for resources
10 10  
... ... @@ -24,12 +24,13 @@
24 24  
25 25  (% class="code" %)
26 26  (((
28 +
27 27  . mamba-init (. is important! never do without, this can crash your FastX)
28 28  \\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
29 29  )))
30 30  
31 31  
32 -spyder &
34 +spyder &
33 33  \\~-~-~-~-~-~-
34 34  \\\\Spyder will open.
35 35  
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37 37  
38 38  [[image:attach:image2022-11-1_13-7-14.png||height="250"]]
39 39  
42 +\\
40 40  
41 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 42  
46 +\\
43 43  
44 44  Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
45 45  
50 +\\
46 46  
52 +\\
47 47  
48 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
54 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
55 +\\ =
49 49  
50 -= =
51 -
52 52  **TXM DATA**
53 53  
54 54  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -63,27 +63,29 @@
63 63  
64 64  Continue with next step, "Preparation".
65 65  
71 +\\
66 66  
67 67  **HOLOTOMO DATA**
68 68  
69 69  Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
70 70  
71 -Go to "Load" tab, load processed data.
77 +Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
72 72  
73 -Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
79 +The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
74 74  
75 -Click on "Load processed"
81 +Click on one file and click open
76 76  
77 77  You do not need to load any additional dark images.
78 78  
79 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg.  are still optional. (see below)
85 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
80 80  
81 81  In principle, you can directly proceed to the third tab "Reconstruction". 
82 82  
89 +\\
83 83  
84 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
91 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
85 85  
86 -(**Can be skipped for Holotomography**)
93 +(Can be skipped for Holotomography)
87 87  
88 88  Go to "Prep" tab.
89 89  
... ... @@ -95,26 +95,31 @@
95 95  
96 96  Click "Rotate" button.
97 97  
105 +\\
98 98  
99 99  The following steps are **optional:**
100 100  
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.
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.
102 102  
103 103  **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.
104 104  
105 -**Padding:** RECOMENDED FOR ROI scans! If your samples are significantly __larger__ than the field of view, you can pad your data to prevent artifacts at the outer field of view. Example: 100
113 +**Padding:** If your samples are significantly __larger__ than the field of view, you can pad your data to prevent artifacts at the outer field of view. Example: 100
106 106  
107 107  **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.
108 108  
117 +\\
109 109  
110 110  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
111 111  
121 +\\
112 112  
113 113  **Save current stack.** Writes the normalized projections to your beamtime folder.
114 114  
125 +\\
115 115  
116 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
127 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
117 117  
129 +\\
118 118  
119 119  **Finding the correct center of rotation. **
120 120  
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136 136  
137 137  **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.
138 138  
151 +\\
139 139  
140 140  How does a good rotation center look like?
141 141  
142 -(% class="relative-table wrapped" style="width:37.5112%" %)
155 +(% class="relative-table wrapped" style="width: 57.8179%;" %)
143 143  |=(((
144 144  good
145 145  )))|=(((
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158 158  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
159 159  )))
160 160  )))|(((
161 -
174 +\\
162 162  )))
163 163  |(((
164 164  (% class="content-wrapper" %)
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174 174  The ghosting effect on the edges is due to sample movement during the scan.
175 175  )))
176 176  |(((
177 -
190 +\\
178 178  )))|(((
179 -
192 +\\
180 180  )))|(((
181 -
194 +\\
182 182  )))
183 183  |(((
184 184  (% class="content-wrapper" %)
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191 191  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
192 192  )))
193 193  )))|(((
194 -
207 +\\
195 195  )))
196 196  
197 197  [[image:attach:image2023-1-23_11-39-57.png||height="400"]]
198 198  
212 +\\
199 199  
214 +\\
200 200  
201 201  **Reconstruction Parameters. **
202 202  
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212 212  
213 213  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".
214 214  
230 +\\
215 215  
216 216  When you are happy with your result, press "Reconstruct full stack".
217 217  
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219 219  
220 220  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.
221 221  
238 +\\
222 222  
240 +\\
223 223  
242 +\\
224 224  
225 -
244 +\\
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -236814957
1 +365845773
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/365845773/03a Reconstruction with Reco GUI