Skip to Content
Last modified by flenners on 2026-02-04 17:25
From version 15.1
edited by greving
on 2024-12-12 18:05
Change comment: There is no comment for this version
To version 3.1
edited by flenners
on 2021-12-07 14:38
Change comment: There is no comment for this version

Summary

Details

Page properties
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.greving
1 +XWiki.flenners
Content
... ... @@ -1,55 +48,6 @@
1 -== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2 -
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 48  = {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
49 - =
2 +\\ =
50 50  
51 -**TXM DATA**
52 -
53 53  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
54 54  
55 55  Now, the list of your scans will be shown below under "folder". Below folders, there are darks with different exposure times.
... ... @@ -62,30 +62,14 @@
62 62  
63 63  Continue with next step, "Preparation".
64 64  
16 +\\
65 65  
66 -**HOLOTOMO DATA**
18 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
67 67  
68 -Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
20 +\\
69 69  
70 -Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
22 + Go to "Prep" tab.
71 71  
72 -The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
73 -
74 -Click on one file and click open
75 -
76 -You do not need to load any additional dark images.
77 -
78 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
79 -
80 -In principle, you can directly proceed to the third tab "Reconstruction". 
81 -
82 -
83 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
84 -
85 -(Can be skipped for Holotomography)
86 -
87 -Go to "Prep" tab.
88 -
89 89  The following is usually required for reconstruction:
90 90  
91 91  Click "Normalize" button. This will take several minutes.
... ... @@ -94,10 +94,11 @@
94 94  
95 95  Click "Rotate" button.
96 96  
32 +\\
97 97  
98 98  The following steps are **optional:**
99 99  
100 -**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.
36 +**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.
101 101  
102 102  **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.
103 103  
... ... @@ -105,103 +105,39 @@
105 105  
106 106  **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.
107 107  
44 +\\
108 108  
109 109  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
110 110  
48 +\\
111 111  
112 112  **Save current stack.** Writes the normalized projections to your beamtime folder.
113 113  
52 +\\
114 114  
115 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
54 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
116 116  
56 +\\
117 117  
118 118  **Finding the correct center of rotation. **
119 119  
120 -First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation
60 +First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation.
121 121  
122 -**~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.)
62 +**Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
123 123  
124 -**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. 
64 +**Delta:** Range which is reconstructed. Good starting value is 50. For fine rot center, choose 10. 
125 125  
126 -**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)
66 +**Stepsize:** Stepsize beween the different rotation centers. Good start value is 5 and 1 for fine rot center.
127 127  
128 -**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.)
68 +Slice: Slice which will be reconstructed. You can also check different slices for checking the rotation center.
129 129  
130 -**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.
70 +\\
131 131  
132 -[[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
133 -
134 -in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
135 -
136 -**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.
137 -
138 -
139 -How does a good rotation center look like?
140 -
141 -(% class="relative-table wrapped" style="width:37.5112%" %)
142 -|=(((
143 -good
144 -)))|=(((
145 -bad
146 -)))|=(((
147 -comment
148 -)))
149 -|(((
150 -(% class="content-wrapper" %)
151 -(((
152 -[[image:attach:image2022-11-14_14-17-45.png||height="250"]]
153 -)))
154 -)))|(((
155 -(% class="content-wrapper" %)
156 -(((
157 -[[image:attach:image2022-11-14_14-19-33.png||height="250"]]
158 -)))
159 -)))|(((
160 -
161 -)))
162 -|(((
163 -(% class="content-wrapper" %)
164 -(((
165 -[[image:attach:image2022-11-14_15-16-34.png||height="250"]]
166 -)))
167 -)))|(((
168 -(% class="content-wrapper" %)
169 -(((
170 -[[image:attach:image2022-11-14_15-7-13.png||height="250"]]
171 -)))
172 -)))|(((
173 -The ghosting effect on the edges is due to sample movement during the scan.
174 -)))
175 -|(((
176 -
177 -)))|(((
178 -
179 -)))|(((
180 -
181 -)))
182 -|(((
183 -(% class="content-wrapper" %)
184 -(((
185 -[[image:attach:image2022-11-14_15-29-47.png||height="250"]]
186 -)))
187 -)))|(((
188 -(% class="content-wrapper" %)
189 -(((
190 -**[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
191 -)))
192 -)))|(((
193 -
194 -)))
195 -
196 -[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
197 -
198 -
199 -
200 200  **Reconstruction Parameters. **
201 201  
202 202  When you found the correct rotation center, you can continue with the reconstruction.
203 203  
204 -Enter the final roation center from the above step.
76 +Enter the final roation center from the above step.
205 205  
206 206  You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
207 207  
... ... @@ -211,6 +211,7 @@
211 211  
212 212  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".
213 213  
86 +\\
214 214  
215 215  When you are happy with your result, press "Reconstruct full stack".
216 216  
... ... @@ -218,7 +218,10 @@
218 218  
219 219  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.
220 220  
94 +\\
221 221  
96 +\\
222 222  
98 +\\
223 223  
224 -
100 +\\
image2022-11-14_14-1-39.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.wirtenss
Size
... ... @@ -1,1 +1,0 @@
1 -170.0 KB
Content
image2022-11-14_14-17-45.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.wirtenss
Size
... ... @@ -1,1 +1,0 @@
1 -473.7 KB
Content
image2022-11-14_14-19-33.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.wirtenss
Size
... ... @@ -1,1 +1,0 @@
1 -473.7 KB
Content
image2022-11-14_14-4-49.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.wirtenss
Size
... ... @@ -1,1 +1,0 @@
1 -172.4 KB
Content
image2022-11-14_15-16-34.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.wirtenss
Size
... ... @@ -1,1 +1,0 @@
1 -463.7 KB
Content
image2022-11-14_15-28-50.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.wirtenss
Size
... ... @@ -1,1 +1,0 @@
1 -455.4 KB
Content
image2022-11-14_15-29-47.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.wirtenss
Size
... ... @@ -1,1 +1,0 @@
1 -428.5 KB
Content
image2022-11-14_15-7-13.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.wirtenss
Size
... ... @@ -1,1 +1,0 @@
1 -431.4 KB
Content
image2022-11-1_13-7-14.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.flenners
Size
... ... @@ -1,1 +1,0 @@
1 -165.5 KB
Content
image2023-1-23_11-39-57.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.flenners
Size
... ... @@ -1,1 +1,0 @@
1 -1.4 MB
Content
Confluence.Code.ConfluencePageClass[0]
Id
... ... @@ -1,1 +1,1 @@
1 -236814957
1 +238028287
URL
... ... @@ -1,1 +1,1 @@
1 -https://confluence.desy.de/spaces/P5I/pages/236814957/03a Reconstruction with Reco GUI
1 +https://confluence.desy.de/spaces/P5I/pages/238028287/03a Reconstruction with Reco GUI