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Last modified by flenners on 2026-02-04 17:25
From version 5.1
edited by flenners
on 2022-09-16 09:16
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To version 16.3
edited by flenners
on 2026-02-04 17:16
Change comment: There is no comment for this version

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1 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
2 -\\ =
1 +== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
3 3  
3 +Terminal:
4 +
5 +
6 +salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
7 +\\(if you need gpu: ~-~-partition=psxgpu )
8 +
9 +//Answer~:// salloc: job [//number//] queued and waiting for resources
10 +
11 + salloc: job [number] has been allocated resources
12 +
13 + salloc: Granted job allocation [number]
14 +
15 + salloc: Waiting for resource configuration
16 +
17 + 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)
18 +
19 +(% class="code" %)
20 +(((
21 +ssh max-wn035 (shell to your node)
22 +\\module load maxwell mamba
23 +)))
24 +
25 +(% class="code" %)
26 +(((
27 +. mamba-init (. is important! never do without, this can crash your FastX)
28 +\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
29 +)))
30 +
31 +
32 +spyder &
33 +\\~-~-~-~-~-~-
34 +\\\\Spyder will open.
35 +
36 +On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
37 +
38 +[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
39 +
40 +
41 +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
42 +
43 +
44 +Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
45 +
46 +
47 +
48 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
49 +
50 += =
51 +
4 4  **TXM DATA**
5 5  
6 6  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -15,27 +15,27 @@
15 15  
16 16  Continue with next step, "Preparation".
17 17  
18 -\\
19 19  
20 20  **HOLOTOMO DATA**
21 21  
22 -Hint: you have to perform the phase reconstruction of your projections first!
69 +Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
23 23  
24 -Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
71 +Go to "Load" tab, load processed data.
25 25  
26 -The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
73 +Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
27 27  
75 +Click on "Load processed"
76 +
28 28  You do not need to load any additional dark images.
29 29  
30 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
79 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg.  are still optional. (see below)
31 31  
32 32  In principle, you can directly proceed to the third tab "Reconstruction". 
33 33  
34 -\\
35 35  
36 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
84 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
37 37  
38 -\\
86 +(**Can be skipped for Holotomography**)
39 39  
40 40  Go to "Prep" tab.
41 41  
... ... @@ -47,51 +47,114 @@
47 47  
48 48  Click "Rotate" button.
49 49  
50 -\\
51 51  
52 52  The following steps are **optional:**
53 53  
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.
101 +**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.
55 55  
56 56  **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.
57 57  
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
105 +**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
59 59  
60 60  **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.
61 61  
62 -\\
63 63  
64 64  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
65 65  
66 -\\
67 67  
68 68  **Save current stack.** Writes the normalized projections to your beamtime folder.
69 69  
70 -\\
71 71  
72 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
116 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
73 73  
74 -\\
75 75  
76 76  **Finding the correct center of rotation. **
77 77  
78 -First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation.
121 +First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation
79 79  
80 -**Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
123 +**~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.)
81 81  
82 -**Delta:** Range which is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
125 +**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. 
83 83  
84 -**Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center.
127 +**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)
85 85  
86 -Slice: Slice which will be reconstructed. You can also check different slices for checking the rotation center.
129 +**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.)
87 87  
88 -\\
131 +**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.
89 89  
133 +[[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
134 +
135 +in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
136 +
137 +**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.
138 +
139 +
140 +How does a good rotation center look like?
141 +
142 +(% class="relative-table wrapped" style="width:37.5112%" %)
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174 +The ghosting effect on the edges is due to sample movement during the scan.
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90 90  **Reconstruction Parameters. **
91 91  
92 92  When you found the correct rotation center, you can continue with the reconstruction.
93 93  
94 -Enter the final roation center from the above step.
205 +Enter the final roation center from the above step.
95 95  
96 96  You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
97 97  
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101 101  
102 102  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".
103 103  
104 -\\
105 105  
106 106  When you are happy with your result, press "Reconstruct full stack".
107 107  
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109 109  
110 110  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.
111 111  
112 -\\
113 113  
114 -\\
115 115  
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117 117  
118 -\\
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -275770572
1 +236814957
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/275770572/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/236814957/03a Reconstruction with Reco GUI