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Last modified by flenners on 2026-02-04 17:25
From version 18.1
edited by flenners
on 2026-02-04 17:20
Change comment: Uploaded new attachment "image2021-4-27_13-55-52.png", version {1}
To version 11.1
edited by flenners
on 2023-11-27 14:35
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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 
9 -
10 -
11 -
12 -Terminal:
13 -
14 -
15 -salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
16 -\\(if you need gpu: ~-~-partition=psxgpu )
17 -
18 -//Answer~:// salloc: job [//number//] queued and waiting for resources
19 -
20 - salloc: job [number] has been allocated resources
21 -
22 - salloc: Granted job allocation [number]
23 -
24 - salloc: Waiting for resource configuration
25 -
26 - 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)
27 -
28 -(% class="code" %)
29 -(((
30 -ssh max-wn035 (shell to your node)
31 -\\module load maxwell mamba
32 -)))
33 -
34 -(% class="code" %)
35 -(((
36 -. mamba-init (. is important! never do without, this can crash your FastX)
37 -\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
38 -)))
39 -
40 -
41 -spyder &
42 -\\~-~-~-~-~-~-
43 -\\\\Spyder will open.
44 -
45 -On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
46 -
47 -[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
48 -
49 -
50 -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
51 -
52 -
53 -Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
54 -
55 -
56 -
57 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
58 -
59 -= =
60 -
61 61  **TXM DATA**
62 62  
63 63  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -72,27 +72,29 @@
72 72  
73 73  Continue with next step, "Preparation".
74 74  
18 +\\
75 75  
76 76  **HOLOTOMO DATA**
77 77  
78 -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!
79 79  
80 -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.
81 81  
82 -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_~#~#//
83 83  
84 -Click on "Load processed"
28 +Click on one file and click open
85 85  
86 86  You do not need to load any additional dark images.
87 87  
88 -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)
89 89  
90 90  In principle, you can directly proceed to the third tab "Reconstruction". 
91 91  
36 +\\
92 92  
93 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
38 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
94 94  
95 -(**Can be skipped for Holotomography**)
40 +(Can be skipped for Holotomography)
96 96  
97 97  Go to "Prep" tab.
98 98  
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104 104  
105 105  Click "Rotate" button.
106 106  
52 +\\
107 107  
108 108  The following steps are **optional:**
109 109  
110 -**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.
111 111  
112 112  **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.
113 113  
114 -**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
115 115  
116 116  **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.
117 117  
64 +\\
118 118  
119 119  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
120 120  
68 +\\
121 121  
122 122  **Save current stack.** Writes the normalized projections to your beamtime folder.
123 123  
72 +\\
124 124  
125 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
74 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
126 126  
76 +\\
127 127  
128 128  **Finding the correct center of rotation. **
129 129  
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145 145  
146 146  **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.
147 147  
98 +\\
148 148  
149 149  How does a good rotation center look like?
150 150  
151 -(% class="relative-table wrapped" style="width:37.5112%" %)
102 +(% class="relative-table wrapped" style="width: 57.8179%;" %)
152 152  |=(((
153 153  good
154 154  )))|=(((
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167 167  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
168 168  )))
169 169  )))|(((
170 -
121 +\\
171 171  )))
172 172  |(((
173 173  (% class="content-wrapper" %)
... ... @@ -183,11 +183,11 @@
183 183  The ghosting effect on the edges is due to sample movement during the scan.
184 184  )))
185 185  |(((
186 -
137 +\\
187 187  )))|(((
188 -
139 +\\
189 189  )))|(((
190 -
141 +\\
191 191  )))
192 192  |(((
193 193  (% class="content-wrapper" %)
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200 200  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
201 201  )))
202 202  )))|(((
203 -
154 +\\
204 204  )))
205 205  
206 206  [[image:attach:image2023-1-23_11-39-57.png||height="400"]]
207 207  
159 +\\
208 208  
161 +\\
209 209  
210 210  **Reconstruction Parameters. **
211 211  
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221 221  
222 222  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".
223 223  
177 +\\
224 224  
225 225  When you are happy with your result, press "Reconstruct full stack".
226 226  
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228 228  
229 229  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.
230 230  
185 +\\
231 231  
187 +\\
232 232  
189 +\\
233 233  
234 -
191 +\\
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -236814957
1 +361457340
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/361457340/03a Reconstruction with Reco GUI