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Last modified by flenners on 2026-02-04 17:25
From version 16.2
edited by flenners
on 2026-02-04 17:15
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To version 13.1
edited by flenners
on 2024-05-24 14:55
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1 -== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
1 +== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 2  
3 3  Terminal:
4 4  
5 +\\
5 5  
6 -salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
7 -\\(if you need gpu: ~-~-partition=psxgpu )
7 +salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
8 +\\(if you need gpu: ~-~-constraint=P100 )
8 8  
9 9  //Answer~:// salloc: job [//number//] queued and waiting for resources
10 10  
... ... @@ -24,12 +24,13 @@
24 24  
25 25  (% class="code" %)
26 26  (((
28 +
27 27  . mamba-init (. is important! never do without, this can crash your FastX)
28 28  \\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
29 29  )))
30 30  
31 31  
32 -spyder &
34 +spyder &
33 33  \\~-~-~-~-~-~-
34 34  \\\\Spyder will open.
35 35  
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37 37  
38 38  [[image:attach:image2022-11-1_13-7-14.png||height="250"]]
39 39  
42 +\\
40 40  
41 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 42  
46 +\\
43 43  
44 44  Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
45 45  
50 +\\
46 46  
52 +\\
47 47  
48 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
54 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
55 +\\ =
49 49  
50 -= =
51 -
52 52  **TXM DATA**
53 53  
54 54  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -63,18 +63,18 @@
63 63  
64 64  Continue with next step, "Preparation".
65 65  
71 +\\
66 66  
67 67  **HOLOTOMO DATA**
68 68  
69 69  Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
70 70  
71 -Go to "Load" tab, load processed data.
77 +Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
72 72  
73 -Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
79 +The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
74 74  
75 -Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
81 +Click on one file and click open
76 76  
77 -
78 78  You do not need to load any additional dark images.
79 79  
80 80  Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
... ... @@ -81,10 +81,11 @@
81 81  
82 82  In principle, you can directly proceed to the third tab "Reconstruction". 
83 83  
89 +\\
84 84  
85 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
91 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
86 86  
87 -(**Can be skipped for Holotomography**)
93 +(Can be skipped for Holotomography)
88 88  
89 89  Go to "Prep" tab.
90 90  
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96 96  
97 97  Click "Rotate" button.
98 98  
105 +\\
99 99  
100 100  The following steps are **optional:**
101 101  
102 -**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.
109 +**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.
103 103  
104 104  **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.
105 105  
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107 107  
108 108  **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.
109 109  
117 +\\
110 110  
111 111  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
112 112  
121 +\\
113 113  
114 114  **Save current stack.** Writes the normalized projections to your beamtime folder.
115 115  
125 +\\
116 116  
117 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
127 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
118 118  
129 +\\
119 119  
120 120  **Finding the correct center of rotation. **
121 121  
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137 137  
138 138  **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.
139 139  
151 +\\
140 140  
141 141  How does a good rotation center look like?
142 142  
143 -(% class="relative-table wrapped" style="width:37.5112%" %)
155 +(% class="relative-table wrapped" style="width: 57.8179%;" %)
144 144  |=(((
145 145  good
146 146  )))|=(((
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159 159  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
160 160  )))
161 161  )))|(((
162 -
174 +\\
163 163  )))
164 164  |(((
165 165  (% class="content-wrapper" %)
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175 175  The ghosting effect on the edges is due to sample movement during the scan.
176 176  )))
177 177  |(((
178 -
190 +\\
179 179  )))|(((
180 -
192 +\\
181 181  )))|(((
182 -
194 +\\
183 183  )))
184 184  |(((
185 185  (% class="content-wrapper" %)
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192 192  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
193 193  )))
194 194  )))|(((
195 -
207 +\\
196 196  )))
197 197  
198 198  [[image:attach:image2023-1-23_11-39-57.png||height="400"]]
199 199  
212 +\\
200 200  
214 +\\
201 201  
202 202  **Reconstruction Parameters. **
203 203  
... ... @@ -213,6 +213,7 @@
213 213  
214 214  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".
215 215  
230 +\\
216 216  
217 217  When you are happy with your result, press "Reconstruct full stack".
218 218  
... ... @@ -220,7 +220,10 @@
220 220  
221 221  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.
222 222  
238 +\\
223 223  
240 +\\
224 224  
242 +\\
225 225  
226 -
244 +\\
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Confluence.Code.ConfluencePageClass[0]
Id
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1 -236814957
1 +365845773
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/365845773/03a Reconstruction with Reco GUI