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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 10.1
edited by flenners
on 2023-01-23 11:40
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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 +95,29 @@
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"
28 +Click on one file and click open
108 108  
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)
32 +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  
36 +\\
115 115  
116 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
38 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
117 117  
118 -(**Can be skipped for Holotomography**)
40 +(Can be skipped for Holotomography)
119 119  
120 120  Go to "Prep" tab.
121 121  
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127 127  
128 128  Click "Rotate" button.
129 129  
52 +\\
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.
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.
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
60 +**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  
64 +\\
141 141  
142 142  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
143 143  
68 +\\
144 144  
145 145  **Save current stack.** Writes the normalized projections to your beamtime folder.
146 146  
72 +\\
147 147  
148 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
74 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
149 149  
76 +\\
150 150  
151 151  **Finding the correct center of rotation. **
152 152  
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168 168  
169 169  **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.
170 170  
98 +\\
171 171  
172 172  How does a good rotation center look like?
173 173  
174 -(% class="relative-table wrapped" style="width:37.5112%" %)
102 +(% class="relative-table wrapped" style="width: 57.8179%;" %)
175 175  |=(((
176 176  good
177 177  )))|=(((
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190 190  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
191 191  )))
192 192  )))|(((
193 -
121 +\\
194 194  )))
195 195  |(((
196 196  (% class="content-wrapper" %)
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206 206  The ghosting effect on the edges is due to sample movement during the scan.
207 207  )))
208 208  |(((
209 -
137 +\\
210 210  )))|(((
211 -
139 +\\
212 212  )))|(((
213 -
141 +\\
214 214  )))
215 215  |(((
216 216  (% class="content-wrapper" %)
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223 223  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
224 224  )))
225 225  )))|(((
226 -
154 +\\
227 227  )))
228 228  
229 -[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
157 +[[image:attach:image2023-1-23_11-39-57.png]]
230 230  
159 +\\
231 231  
161 +\\
232 232  
233 233  **Reconstruction Parameters. **
234 234  
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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  
177 +\\
247 247  
248 248  When you are happy with your result, press "Reconstruct full stack".
249 249  
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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  
185 +\\
254 254  
187 +\\
255 255  
189 +\\
256 256  
257 -
191 +\\
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -236814957
1 +334843410
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/334843410/03a Reconstruction with Reco GUI