Changes for page 03a Reconstruction with Reco GUI

Summary

• Page properties (2 modified, 0 added, 0 removed)

Details

Page properties

Author

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1		-XWiki.flenners
	1	+XWiki.greving

Content

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1		-== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
	1	+== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation: ==
2	2
3	3	Terminal:
4	4
5		-\\
6	6
7		-salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
8		-\\(if you need gpu: ~-~-constraint=P100 )
	6	+salloc ~-~-partition=psxcpu ~-~-nodes=1 ~-~-time=06:00:00
	7	+\\(if you need gpu: ~-~-partition=psxgpu )
9	9
10	10	//Answer~:// salloc: job [//number//] queued and waiting for resources
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25	25
26	26	(% class="code" %)
27	27	(((
28		-
29	29	. mamba-init (. is important! never do without, this can crash your FastX)
30	30	\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
31	31	)))
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33	33
34		-spyder &
	32	+spyder &
35	35	\\~-~-~-~-~-~-
36	36	\\\\Spyder will open.
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39	39
40	40	[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
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42		-\\
43	43
44	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	45
46		-\\
47	47
48	48	Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
49	49
50		-\\
51	51
52		-\\
53	53
54	54	= {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
55		-\\ =
	49	+ =
56	56
57	57	**TXM DATA**
58	58
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68	68
69	69	Continue with next step, "Preparation".
70	70
71		-\\
72	72
73	73	**HOLOTOMO DATA**
74	74
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86	86
87	87	In principle, you can directly proceed to the third tab "Reconstruction".
88	88
89		-\\
90	90
91		-= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
	83	+= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction =
92	92
93	93	(Can be skipped for Holotomography)
94	94
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102	102
103	103	Click "Rotate" button.
104	104
105		-\\
106	106
107	107	The following steps are **optional:**
108	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.
	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.
110	110
111	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.
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115	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	116
117		-\\
118	118
119	119	**Linogram alignment:** Linogram alignment if sample moved. Ask your local contact if this is necessary.
120	120
121		-\\
122	122
123	123	**Save current stack.** Writes the normalized projections to your beamtime folder.
124	124
125		-\\
126	126
127		-= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
	115	+= {{id name="03aReconstructionwithRecoGUI-Reconstruction"/}}Reconstruction =
128	128
129		-\\
130	130
131	131	**Finding the correct center of rotation. **
132	132
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148	148
149	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	150
151		-\\
152	152
153	153	How does a good rotation center look like?
154	154
155		-(% class="relative-table wrapped" style="width: 37.5112%;" %)
	141	+(% class="relative-table wrapped" style="width:37.5112%" %)
156	156	|=(((
157	157	good
158	158	)))|=(((
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171	171	[[image:attach:image2022-11-14_14-19-33.png||height="250"]]
172	172	)))
173	173	)))|(((
174		-\\
	160	+
175	175	)))
176	176	|(((
177	177	(% class="content-wrapper" %)
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187	187	The ghosting effect on the edges is due to sample movement during the scan.
188	188	)))
189	189	|(((
190		-\\
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191	191	)))|(((
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195	195	)))
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197	197	(% class="content-wrapper" %)
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204	204	**[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
205	205	)))
206	206	)))|(((
207		-\\
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208	208	)))
209	209
210	210	[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
211	211
212		-\\
213	213
214		-\\
215	215
216	216	**Reconstruction Parameters. **
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227	227
228	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	229
230		-\\
231	231
232	232	When you are happy with your result, press "Reconstruct full stack".
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236	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	237
238		-\\
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244		-\\
	224	+