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Last modified by flenners on 2026-02-04 17:25
From version 20.1
edited by flenners
on 2026-02-04 17:25
Change comment: There is no comment for this version
To version 11.1
edited by flenners
on 2023-11-27 14:35
Change comment: There is no comment for this version

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1 -== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
1 += {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
2 +\\ =
2 2  
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 -Open a terminal:
14 -
15 -[[image:1770222205178-264.png]]
16 -
17 -
18 -In this terminal, type:
19 -
20 -{{{salloc --partition=psxcpu --nodes=1 --time=06:00:00}}}
21 -
22 -(((
23 -
24 -)))
25 -
26 -(((
27 -//(if you need gpu: ~-~-partition=psxgpu )//
28 -)))
29 -
30 -(((
31 -//Answer: salloc: job [number] queued and waiting for resources//
32 -)))
33 -
34 -(((
35 -// salloc: job [number] has been allocated resources//
36 -)))
37 -
38 -(((
39 -// salloc: Granted job allocation [number]//
40 -)))
41 -
42 -(((
43 -// salloc: Waiting for resource configuration//
44 -)))
45 -
46 -(((
47 -// 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)//
48 -)))
49 -
50 -(% class="code" %)
51 -(((
52 -(((
53 -
54 -)))
55 -
56 -(((
57 -ssh max-wn035 (shell to your node)
58 -\\module load maxwell mamba
59 -)))
60 -)))
61 -
62 -(% class="code" %)
63 -(((
64 -. mamba-init (. is important! never do without, this can crash your FastX)
65 -\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
66 -)))
67 -
68 -{{{spyder &
69 -
70 -------
71 -
72 -
73 -Spyder will open. }}}
74 -
75 -On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
76 -
77 -[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
78 -
79 -
80 -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
81 -
82 -
83 -Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
84 -
85 -
86 -
87 -= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data =
88 -
89 -= =
90 -
91 91  **TXM DATA**
92 92  
93 93  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
... ... @@ -102,27 +102,29 @@
102 102  
103 103  Continue with next step, "Preparation".
104 104  
18 +\\
105 105  
106 106  **HOLOTOMO DATA**
107 107  
108 -Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
22 +Hint: you have to perform the phase reconstruction of your projections first!
109 109  
110 -Go to "Load" tab, load processed data.
24 +Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
111 111  
112 -Check the subfolder path of the phase retievals. Standard path is holopipe/phase_retrieval
26 +The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
113 113  
114 -Click on "Load processed"
28 +Click on one file and click open
115 115  
116 116  You do not need to load any additional dark images.
117 117  
118 -Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps, eg. padding are still optional. (see below)
32 +Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
119 119  
120 120  In principle, you can directly proceed to the third tab "Reconstruction". 
121 121  
36 +\\
122 122  
123 -= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
38 += {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
124 124  
125 -(**Can be skipped for Holotomography**)
40 +(Can be skipped for Holotomography)
126 126  
127 127  Go to "Prep" tab.
128 128  
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134 134  
135 135  Click "Rotate" button.
136 136  
52 +\\
137 137  
138 138  The following steps are **optional:**
139 139  
140 -**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.
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.
141 141  
142 142  **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.
143 143  
144 -**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
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
145 145  
146 146  **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.
147 147  
64 +\\
148 148  
149 149  **Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
150 150  
68 +\\
151 151  
152 152  **Save current stack.** Writes the normalized projections to your beamtime folder.
153 153  
72 +\\
154 154  
155 -= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
74 += {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
156 156  
76 +\\
157 157  
158 158  **Finding the correct center of rotation. **
159 159  
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175 175  
176 176  **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.
177 177  
98 +\\
178 178  
179 179  How does a good rotation center look like?
180 180  
181 -(% class="relative-table wrapped" style="width:37.5112%" %)
102 +(% class="relative-table wrapped" style="width: 57.8179%;" %)
182 182  |=(((
183 183  good
184 184  )))|=(((
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197 197  [[image:attach:image2022-11-14_14-19-33.png||height="250"]]
198 198  )))
199 199  )))|(((
200 -
121 +\\
201 201  )))
202 202  |(((
203 203  (% class="content-wrapper" %)
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213 213  The ghosting effect on the edges is due to sample movement during the scan.
214 214  )))
215 215  |(((
216 -
137 +\\
217 217  )))|(((
218 -
139 +\\
219 219  )))|(((
220 -
141 +\\
221 221  )))
222 222  |(((
223 223  (% class="content-wrapper" %)
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230 230  **[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
231 231  )))
232 232  )))|(((
233 -
154 +\\
234 234  )))
235 235  
236 236  [[image:attach:image2023-1-23_11-39-57.png||height="400"]]
237 237  
159 +\\
238 238  
161 +\\
239 239  
240 240  **Reconstruction Parameters. **
241 241  
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251 251  
252 252  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".
253 253  
177 +\\
254 254  
255 255  When you are happy with your result, press "Reconstruct full stack".
256 256  
... ... @@ -258,7 +258,10 @@
258 258  
259 259  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.
260 260  
185 +\\
261 261  
187 +\\
262 262  
189 +\\
263 263  
264 -
191 +\\
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Content
Confluence.Code.ConfluencePageClass[0]
Id
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1 -236814957
1 +361457340
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/361457340/03a Reconstruction with Reco GUI