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Last modified by flenners on 2026-02-04 17:25
From version 18.3
edited by flenners
on 2026-02-04 17:23
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To version 14.1
edited by flenners
on 2024-06-25 11:43
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 -
4 -Open the following link in a browser and log in with your DESY account (not door account!).
5 -
6 -[[https:~~/~~/max-display.desy.de:3389/auth/ssh>>url:https://max-display.desy.de:3443/auth/ssh]]
7 -
8 -Start a new XFCE session by clicking on the running mouse:, select browser session
9 -
10 -[[image:image2021-4-27_13-55-52.png||height="405" width="911"]]
11 -
12 -
13 -
14 14  Terminal:
15 15  
5 +\\
16 16  
17 -salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
18 -\\(if you need gpu: ~-~-partition=psxgpu )
7 +salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
8 +\\(if you need gpu: ~-~-constraint=P100 )
19 19  
20 20  //Answer~:// salloc: job [//number//] queued and waiting for resources
21 21  
... ... @@ -35,12 +35,13 @@
35 35  
36 36  (% class="code" %)
37 37  (((
28 +
38 38  . mamba-init (. is important! never do without, this can crash your FastX)
39 39  \\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
40 40  )))
41 41  
42 42  
43 -spyder &
34 +spyder &
44 44  \\~-~-~-~-~-~-
45 45  \\\\Spyder will open.
46 46  
... ... @@ -48,18 +48,21 @@
48 48  
49 49  [[image:attach:image2022-11-1_13-7-14.png||height="250"]]
50 50  
42 +\\
51 51  
52 52  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
53 53  
46 +\\
54 54  
55 55  Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
56 56  
50 +\\
57 57  
52 +\\
58 58  
59 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
54 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
55 +\\ =
60 60  
61 -= =
62 -
63 63  **TXM DATA**
64 64  
65 65  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -74,27 +74,29 @@
74 74  
75 75  Continue with next step, "Preparation".
76 76  
71 +\\
77 77  
78 78  **HOLOTOMO DATA**
79 79  
80 80  Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
81 81  
82 -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.
83 83  
84 -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_~#~#//
85 85  
86 -Click on "Load processed"
81 +Click on one file and click open
87 87  
88 88  You do not need to load any additional dark images.
89 89  
90 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg. padding are still optional. (see below)
85 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
91 91  
92 92  In principle, you can directly proceed to the third tab "Reconstruction". 
93 93  
89 +\\
94 94  
95 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
91 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
96 96  
97 -(**Can be skipped for Holotomography**)
93 +(Can be skipped for Holotomography)
98 98  
99 99  Go to "Prep" tab.
100 100  
... ... @@ -106,26 +106,31 @@
106 106  
107 107  Click "Rotate" button.
108 108  
105 +\\
109 109  
110 110  The following steps are **optional:**
111 111  
112 -**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.
113 113  
114 114  **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.
115 115  
116 -**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
117 117  
118 118  **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.
119 119  
117 +\\
120 120  
121 121  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
122 122  
121 +\\
123 123  
124 124  **Save current stack.** Writes the normalized projections to your beamtime folder.
125 125  
125 +\\
126 126  
127 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
127 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
128 128  
129 +\\
129 129  
130 130  **Finding the correct center of rotation. **
131 131  
... ... @@ -147,10 +147,11 @@
147 147  
148 148  **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.
149 149  
151 +\\
150 150  
151 151  How does a good rotation center look like?
152 152  
153 -(% class="relative-table wrapped" style="width:37.5112%" %)
155 +(% class="relative-table wrapped" style="width: 37.5112%;" %)
154 154  |=(((
155 155  good
156 156  )))|=(((
... ... @@ -169,7 +169,7 @@
169 169  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
170 170  )))
171 171  )))|(((
172 -
174 +\\
173 173  )))
174 174  |(((
175 175  (% class="content-wrapper" %)
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185 185  The ghosting effect on the edges is due to sample movement during the scan.
186 186  )))
187 187  |(((
188 -
190 +\\
189 189  )))|(((
190 -
192 +\\
191 191  )))|(((
192 -
194 +\\
193 193  )))
194 194  |(((
195 195  (% class="content-wrapper" %)
... ... @@ -202,12 +202,14 @@
202 202  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
203 203  )))
204 204  )))|(((
205 -
207 +\\
206 206  )))
207 207  
208 208  [[image:attach:image2023-1-23_11-39-57.png||height="400"]]
209 209  
212 +\\
210 210  
214 +\\
211 211  
212 212  **Reconstruction Parameters. **
213 213  
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223 223  
224 224  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".
225 225  
230 +\\
226 226  
227 227  When you are happy with your result, press "Reconstruct full stack".
228 228  
... ... @@ -230,7 +230,10 @@
230 230  
231 231  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.
232 232  
238 +\\
233 233  
240 +\\
234 234  
242 +\\
235 235  
236 -
244 +\\
image2021-4-27_13-55-52.png
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1 -XWiki.flenners
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