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Last modified by flenners on 2026-02-04 17:25
From version 20.1
edited by flenners
on 2026-02-04 17:25
Change comment: There is no comment for this version
To version 5.1
edited by flenners
on 2022-09-16 09:16
Change comment: There is no comment for this version

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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 -
18 -In this terminal, type:
19 -
20 -{{{salloc --partition=psxcpu --nodes=1 --time=06:00:00}}}
21 -
22 -(((
23 -
24 -)))
25 -
26 -(((
27 -//(if you need gpu: ~-~-partition=psxgpu )//
28 -)))
29 -
30 -(((
31 -//Answer: salloc: job [number] queued and waiting for resources//
32 -)))
33 -
34 -(((
35 -// salloc: job [number] has been allocated resources//
36 -)))
37 -
38 -(((
39 -// salloc: Granted job allocation [number]//
40 -)))
41 -
42 -(((
43 -// salloc: Waiting for resource configuration//
44 -)))
45 -
46 -(((
47 -// 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)//
48 -)))
49 -
50 -(% class="code" %)
51 -(((
52 -(((
53 -
54 -)))
55 -
56 -(((
57 -ssh max-wn035 (shell to your node)
58 -\\module load maxwell mamba
59 -)))
60 -)))
61 -
62 -(% class="code" %)
63 -(((
64 -. mamba-init (. is important! never do without, this can crash your FastX)
65 -\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
66 -)))
67 -
68 -{{{spyder &
69 -
70 -------
71 -
72 -
73 -Spyder will open. }}}
74 -
75 -On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
76 -
77 -[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
78 -
79 -
80 -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
81 -
82 -
83 -Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
84 -
85 -
86 -
87 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
88 -
89 -= =
90 -
91 91  **TXM DATA**
92 92  
93 93  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -102,27 +102,27 @@
102 102  
103 103  Continue with next step, "Preparation".
104 104  
18 +\\
105 105  
106 106  **HOLOTOMO DATA**
107 107  
108 -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!
109 109  
110 -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.
111 111  
112 -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_~#~#//
113 113  
114 -Click on "Load processed"
115 -
116 116  You do not need to load any additional dark images.
117 117  
118 -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)
119 119  
120 120  In principle, you can directly proceed to the third tab "Reconstruction". 
121 121  
34 +\\
122 122  
123 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
36 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
124 124  
125 -(**Can be skipped for Holotomography**)
38 +\\
126 126  
127 127  Go to "Prep" tab.
128 128  
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134 134  
135 135  Click "Rotate" button.
136 136  
50 +\\
137 137  
138 138  The following steps are **optional:**
139 139  
140 -**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.
141 141  
142 142  **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.
143 143  
144 -**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
145 145  
146 146  **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.
147 147  
62 +\\
148 148  
149 149  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
150 150  
66 +\\
151 151  
152 152  **Save current stack.** Writes the normalized projections to your beamtime folder.
153 153  
70 +\\
154 154  
155 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
72 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
156 156  
74 +\\
157 157  
158 158  **Finding the correct center of rotation. **
159 159  
160 -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.
161 161  
162 -**~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.)
163 163  
164 -**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. 
165 165  
166 -**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.
167 167  
168 -**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.
169 169  
170 -**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 +\\
171 171  
172 -[[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
173 -
174 -in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
175 -
176 -**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.
177 -
178 -
179 -How does a good rotation center look like?
180 -
181 -(% class="relative-table wrapped" style="width:37.5112%" %)
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210 -[[image:attach:image2022-11-14_15-7-13.png||height="250"]]
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213 -The ghosting effect on the edges is due to sample movement during the scan.
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236 -[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
237 -
238 -
239 -
240 240  **Reconstruction Parameters. **
241 241  
242 242  When you found the correct rotation center, you can continue with the reconstruction.
243 243  
244 -Enter the final roation center from the above step.
94 +Enter the final roation center from the above step.
245 245  
246 246  You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
247 247  
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251 251  
252 252  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".
253 253  
104 +\\
254 254  
255 255  When you are happy with your result, press "Reconstruct full stack".
256 256  
... ... @@ -258,7 +258,10 @@
258 258  
259 259  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.
260 260  
112 +\\
261 261  
114 +\\
262 262  
116 +\\
263 263  
264 -
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