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Last modified by flenners on 2026-02-04 17:25
From version 9.1
edited by wirtenss
on 2022-11-29 10:25
Change comment: There is no comment for this version
To version 18.3
edited by flenners
on 2026-02-04 17:23
Change comment: There is no comment for this version

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1 -XWiki.wirtenss
1 +XWiki.flenners
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1 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
2 -\\ =
1 +== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
3 3  
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 +
14 +Terminal:
15 +
16 +
17 +salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
18 +\\(if you need gpu: ~-~-partition=psxgpu )
19 +
20 +//Answer~:// salloc: job [//number//] queued and waiting for resources
21 +
22 + salloc: job [number] has been allocated resources
23 +
24 + salloc: Granted job allocation [number]
25 +
26 + salloc: Waiting for resource configuration
27 +
28 + 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)
29 +
30 +(% class="code" %)
31 +(((
32 +ssh max-wn035 (shell to your node)
33 +\\module load maxwell mamba
34 +)))
35 +
36 +(% class="code" %)
37 +(((
38 +. mamba-init (. is important! never do without, this can crash your FastX)
39 +\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
40 +)))
41 +
42 +
43 +spyder &
44 +\\~-~-~-~-~-~-
45 +\\\\Spyder will open.
46 +
47 +On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
48 +
49 +[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
50 +
51 +
52 +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
53 +
54 +
55 +Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
56 +
57 +
58 +
59 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
60 +
61 += =
62 +
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.
... ... @@ -15,29 +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!
80 +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.
82 +Go to "Load" tab, load processed data.
25 25  
26 -The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
84 +Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
27 27  
28 -Click on one file and click open
86 +Click on "Load processed"
29 29  
30 30  You do not need to load any additional dark images.
31 31  
32 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
90 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg. padding are still optional. (see below)
33 33  
34 34  In principle, you can directly proceed to the third tab "Reconstruction". 
35 35  
36 -\\
37 37  
38 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
95 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
39 39  
40 -(Can be skipped for Holotomography)
97 +(**Can be skipped for Holotomography**)
41 41  
42 42  Go to "Prep" tab.
43 43  
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49 49  
50 50  Click "Rotate" button.
51 51  
52 -\\
53 53  
54 54  The following steps are **optional:**
55 55  
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.
112 +**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.
57 57  
58 58  **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.
59 59  
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
116 +**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
61 61  
62 62  **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.
63 63  
64 -\\
65 65  
66 66  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
67 67  
68 -\\
69 69  
70 70  **Save current stack.** Writes the normalized projections to your beamtime folder.
71 71  
72 -\\
73 73  
74 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
127 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
75 75  
76 -\\
77 77  
78 78  **Finding the correct center of rotation. **
79 79  
... ... @@ -95,11 +95,10 @@
95 95  
96 96  **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.
97 97  
98 -\\
99 99  
100 100  How does a good rotation center look like?
101 101  
102 -(% class="relative-table wrapped" style="width: 57.8179%;" %)
153 +(% class="relative-table wrapped" style="width:37.5112%" %)
103 103  |=(((
104 104  good
105 105  )))|=(((
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118 118  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
119 119  )))
120 120  )))|(((
121 -\\
172 +
122 122  )))
123 123  |(((
124 124  (% class="content-wrapper" %)
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134 134  The ghosting effect on the edges is due to sample movement during the scan.
135 135  )))
136 136  |(((
188 +
189 +)))|(((
190 +
191 +)))|(((
192 +
193 +)))
194 +|(((
137 137  (% class="content-wrapper" %)
138 138  (((
139 139  [[image:attach:image2022-11-14_15-29-47.png||height="250"]]
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144 144  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
145 145  )))
146 146  )))|(((
147 -\\
205 +
148 148  )))
149 149  
150 -\\
208 +[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
151 151  
152 -\\
153 153  
154 -\\
155 155  
156 156  **Reconstruction Parameters. **
157 157  
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167 167  
168 168  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".
169 169  
170 -\\
171 171  
172 172  When you are happy with your result, press "Reconstruct full stack".
173 173  
... ... @@ -175,10 +175,7 @@
175 175  
176 176  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.
177 177  
178 -\\
179 179  
180 -\\
181 181  
182 -\\
183 183  
184 -\\
236 +
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -293405975
1 +236814957
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/293405975/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/236814957/03a Reconstruction with Reco GUI