Skip to Content
Version 13.1 by flenners on 2024-05-24 14:55
Hide last authors
flenners 13.1 1 == {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2
3 Terminal:
4
5 \\
6
7 salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
8 \\(if you need gpu: ~-~-constraint=P100 )
9
10 //Answer~:// salloc: job [//number//] queued and waiting for resources
11
12 salloc: job [number] has been allocated resources
13
14 salloc: Granted job allocation [number]
15
16 salloc: Waiting for resource configuration
17
18 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)
19
20 (% class="code" %)
21 (((
22 ssh max-wn035 (shell to your node)
23 \\module load maxwell mamba
24 )))
25
26 (% class="code" %)
27 (((
28
29 . mamba-init (. is important! never do without, this can crash your FastX)
30 \\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
31 )))
32
33
34 spyder &
35 \\~-~-~-~-~-~-
36 \\\\Spyder will open.
37
38 On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
39
40 [[image:attach:image2022-11-1_13-7-14.png||height="250"]]
41
42 \\
43
44 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
45
46 \\
47
48 Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
49
50 \\
51
52 \\
53
flenners 2.1 54 = {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
55 \\ =
56
flenners 4.1 57 **TXM DATA**
58
flenners 2.1 59 Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
60
61 Now, the list of your scans will be shown below under "folder". Below folders, there are darks with different exposure times.
62
63 Select the scan you want to reconstruct and choose the corresponding dark images.
64
65 If you recorded your data after 2019, you can directly continue by clicking the "Load" button. This will read all data needed for reconstruction.
66
67 Loading the data can take some time (usually several minutes). The GUI will be blocked during this time.
68
flenners 3.1 69 Continue with next step, "Preparation".
flenners 2.1 70
71 \\
72
flenners 4.1 73 **HOLOTOMO DATA**
74
flenners 12.1 75 Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
flenners 4.1 76
flenners 5.1 77 Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
flenners 4.1 78
flenners 5.1 79 The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
80
wirtenss 9.1 81 Click on one file and click open
82
flenners 5.1 83 You do not need to load any additional dark images.
84
85 Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
86
87 In principle, you can directly proceed to the third tab "Reconstruction". 
88
89 \\
90
flenners 2.1 91 = {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
92
flenners 6.1 93 (Can be skipped for Holotomography)
flenners 2.1 94
flenners 4.1 95 Go to "Prep" tab.
flenners 2.1 96
97 The following is usually required for reconstruction:
98
99 Click "Normalize" button. This will take several minutes.
100
101 Click "Minus Log" button.
102
103 Click "Rotate" button.
104
105 \\
106
107 The following steps are **optional:**
108
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.
110
111 **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.
112
113 **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
114
115 **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.
116
117 \\
118
119 **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
120
121 \\
122
123 **Save current stack.** Writes the normalized projections to your beamtime folder.
124
125 \\
126
127 = {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
128
129 \\
130
131 **Finding the correct center of rotation. **
132
wirtenss 7.1 133 First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation
flenners 2.1 134
wirtenss 7.1 135 **~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.)
flenners 2.1 136
wirtenss 7.1 137 **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. 
flenners 2.1 138
wirtenss 7.1 139 **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)
flenners 3.1 140
wirtenss 7.1 141 **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.)
flenners 3.1 142
wirtenss 7.1 143 **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.
144
145 [[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
146
147 in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
148
149 **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.
150
flenners 2.1 151 \\
152
wirtenss 8.1 153 How does a good rotation center look like?
154
wirtenss 9.1 155 (% class="relative-table wrapped" style="width: 57.8179%;" %)
wirtenss 8.1 156 |=(((
157 good
158 )))|=(((
159 bad
160 )))|=(((
161 comment
162 )))
163 |(((
164 (% class="content-wrapper" %)
165 (((
166 [[image:attach:image2022-11-14_14-17-45.png||height="250"]]
167 )))
168 )))|(((
169 (% class="content-wrapper" %)
170 (((
171 [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
172 )))
173 )))|(((
wirtenss 7.1 174 \\
wirtenss 8.1 175 )))
176 |(((
177 (% class="content-wrapper" %)
178 (((
179 [[image:attach:image2022-11-14_15-16-34.png||height="250"]]
180 )))
181 )))|(((
182 (% class="content-wrapper" %)
183 (((
184 [[image:attach:image2022-11-14_15-7-13.png||height="250"]]
185 )))
186 )))|(((
187 The ghosting effect on the edges is due to sample movement during the scan.
188 )))
189 |(((
flenners 10.1 190 \\
191 )))|(((
192 \\
193 )))|(((
194 \\
195 )))
196 |(((
wirtenss 8.1 197 (% class="content-wrapper" %)
198 (((
199 [[image:attach:image2022-11-14_15-29-47.png||height="250"]]
200 )))
201 )))|(((
202 (% class="content-wrapper" %)
203 (((
204 **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
205 )))
206 )))|(((
207 \\
208 )))
wirtenss 7.1 209
flenners 11.1 210 [[image:attach:image2023-1-23_11-39-57.png||height="400"]]
wirtenss 7.1 211
wirtenss 8.1 212 \\
213
214 \\
215
flenners 3.1 216 **Reconstruction Parameters. **
217
218 When you found the correct rotation center, you can continue with the reconstruction.
219
wirtenss 7.1 220 Enter the final roation center from the above step.
flenners 3.1 221
222 You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
223
224 You can also add ring removal (can take very long!!!!)
225
226 Mask: If you like a circular mask around your data, check this box.
227
228 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".
229
flenners 2.1 230 \\
231
flenners 3.1 232 When you are happy with your result, press "Reconstruct full stack".
233
234 You can check the data in ImageJ, and if you are not happy, you can also reconstruct with different parameters/ rotation centers.
235
236 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.
237
flenners 2.1 238 \\
flenners 3.1 239
240 \\
241
242 \\
243
244 \\