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Last modified by flenners on 2026-02-04 17:25
From version 19.2
edited by flenners
on 2026-02-04 17:24
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To version 5.1
edited by flenners
on 2022-09-16 09:16
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1 -== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
1 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
2 +\\ =
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 -Open a terminal:
14 -
15 -[[image:1770222205178-264.png]]
16 -
17 -In this terminal, type:
18 -
19 -{{{salloc --partition=psxcpu --nodes=1 --time=06:00:00}}}
20 -
21 -(((
22 -
23 -)))
24 -
25 -(((
26 -(if you need gpu: ~-~-partition=psxgpu )
27 -)))
28 -
29 -(((
30 -//Answer~:// salloc: job [//number//] queued and waiting for resources
31 -)))
32 -
33 -(((
34 - salloc: job [number] has been allocated resources
35 -)))
36 -
37 -(((
38 - salloc: Granted job allocation [number]
39 -)))
40 -
41 -(((
42 - salloc: Waiting for resource configuration
43 -)))
44 -
45 -(((
46 - 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)
47 -)))
48 -
49 -(% class="code" %)
50 -(((
51 -(((
52 -ssh max-wn035 (shell to your node)
53 -\\module load maxwell mamba
54 -)))
55 -)))
56 -
57 -(% class="code" %)
58 -(((
59 -. mamba-init (. is important! never do without, this can crash your FastX)
60 -\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
61 -)))
62 -
63 -
64 -spyder &
65 -\\~-~-~-~-~-~-
66 -\\\\Spyder will open.
67 -
68 -On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
69 -
70 -[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
71 -
72 -
73 -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
74 -
75 -
76 -Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
77 -
78 -
79 -
80 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
81 -
82 -= =
83 -
84 84  **TXM DATA**
85 85  
86 86  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -95,27 +95,27 @@
95 95  
96 96  Continue with next step, "Preparation".
97 97  
18 +\\
98 98  
99 99  **HOLOTOMO DATA**
100 100  
101 -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!
102 102  
103 -Go to "Load" tab, load processed data.
24 +Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
104 104  
105 -Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
26 +The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
106 106  
107 -Click on "Load processed"
108 -
109 109  You do not need to load any additional dark images.
110 110  
111 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg. padding are still optional. (see below)
30 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
112 112  
113 113  In principle, you can directly proceed to the third tab "Reconstruction". 
114 114  
34 +\\
115 115  
116 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
36 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
117 117  
118 -(**Can be skipped for Holotomography**)
38 +\\
119 119  
120 120  Go to "Prep" tab.
121 121  
... ... @@ -127,114 +127,51 @@
127 127  
128 128  Click "Rotate" button.
129 129  
50 +\\
130 130  
131 131  The following steps are **optional:**
132 132  
133 -**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.
54 +**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.
134 134  
135 135  **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.
136 136  
137 -**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
58 +**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
138 138  
139 139  **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.
140 140  
62 +\\
141 141  
142 142  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
143 143  
66 +\\
144 144  
145 145  **Save current stack.** Writes the normalized projections to your beamtime folder.
146 146  
70 +\\
147 147  
148 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
72 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
149 149  
74 +\\
150 150  
151 151  **Finding the correct center of rotation. **
152 152  
153 -First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation
78 +First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation.
154 154  
155 -**~1. Rot center: **Defines the rotation center in pixel coordinates. For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
80 +**Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
156 156  
157 -**2. Delta: **Range of pixels around the in step 1 given rot center for which the test slice is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
82 +**Delta:** Range which is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
158 158  
159 -**3. Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center. (for example [ ... , 507, 512, 517, ... ] for a stepsize of 5)
84 +**Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center.
160 160  
161 -**4. Slice:** Defines the pixel row which is used to reconstruct the test slice. Tip: Choose a region where you expect to see distinctive structures. (You can also check different slices for checking the rotation center.)
86 +Slice: Slice which will be reconstructed. You can also check different slices for checking the rotation center.
162 162  
163 -**5. Check rotation center: **Click on the "Check rotation center" button.** **In the preview window move the slider around until you find the positions with the least artifacts. Remember the position number and check the Spyder Console to get the new rot center coordinates in pixel.
88 +\\
164 164  
165 -[[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
166 -
167 -in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
168 -
169 -**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.
170 -
171 -
172 -How does a good rotation center look like?
173 -
174 -(% class="relative-table wrapped" style="width:37.5112%" %)
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203 -[[image:attach:image2022-11-14_15-7-13.png||height="250"]]
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206 -The ghosting effect on the edges is due to sample movement during the scan.
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229 -[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
230 -
231 -
232 -
233 233  **Reconstruction Parameters. **
234 234  
235 235  When you found the correct rotation center, you can continue with the reconstruction.
236 236  
237 -Enter the final roation center from the above step.
94 +Enter the final roation center from the above step.
238 238  
239 239  You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
240 240  
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244 244  
245 245  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".
246 246  
104 +\\
247 247  
248 248  When you are happy with your result, press "Reconstruct full stack".
249 249  
... ... @@ -251,7 +251,10 @@
251 251  
252 252  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.
253 253  
112 +\\
254 254  
114 +\\
255 255  
116 +\\
256 256  
257 -
118 +\\
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -236814957
1 +275770572
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/275770572/03a Reconstruction with Reco GUI