Changes for page 03a Reconstruction with Reco GUI

Last modified by flenners on 2026-02-04 17:25

From 2.1 to 1.1 From 14.1 to 13.1

From version 13.1

edited by flenners
on 2024-05-24 14:55

Change comment: There is no comment for this version

To version 2.1

edited by flenners
on 2021-12-07 14:27

Change comment: There is no comment for this version

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@@ -1,61 +54,6 @@
--== {{id name="03aReconstructionwithRecoGUI-Preperation:"/}}Preperation:  ==
--
--Terminal:
--
--\\
--
--salloc ~-~-partition=psx ~-~-nodes=1 ~-~-time=06:00:00
--\\(if you need gpu: ~-~-constraint=P100 )
--
--//Answer~:// salloc: job [//number//] queued and waiting for resources
--
--        salloc: job [number] has been allocated resources
--
--        salloc: Granted job allocation [number]
--
--        salloc: Waiting for resource configuration
--
--        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)
--
--(% class="code" %)
--(((
--ssh max-wn035 (shell to your node)
--\\module load maxwell mamba
--)))
--
--(% class="code" %)
--(((
--
--. mamba-init (. is important! never do without, this can crash your FastX)
--\\mamba activate /asap3/petra3/gpfs/common/p05/nano/envs/mamba
--)))
--
--
--spyder &
--\\~-~-~-~-~-~-
--\\\\Spyder will open.
--
--On the right, choose "file explorer". Navigate to your beamtime folder and find processed/scripts/RecoGUI:
--
--[[image:attach:image2022-11-1_13-7-14.png||height="250"]]
--
--\\
--
--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
--
--\\
--
--Open RecoGUI.py by double clicking the file and click "Run" (green arrow)
--
--\\
--
--\\
--
  = {{id name="03aReconstructionwithRecoGUI-LoadingData"/}}Loading Data
  \\ =
--**TXM DATA**
--
  Go to "Load' tab and select year, enter your beamtime ID (e.g. 11001234) and press "enter" on keyboard.
  Now, the list of your scans will be shown below under "folder". Below folders, there are darks with different exposure times.
@@ -66,34 +66,16 @@
  Loading the data can take some time (usually several minutes). The GUI will be blocked during this time.
--Continue with next step, "Preparation".
++Continue with next step, "Preparation"
  \\
--**HOLOTOMO DATA**
++= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction  =
--Hint: you have to perform the phase reconstruction of your projections first! This is usually done by beamline staff. Then you can continue:
--
--Go to "Load" tab. Click on "Load normalized data" at the bottom of the page and select your phase reconstruced projections.
--
--The common path is: ///asap3/petra3/gpfs/p05/YEAR/data/BEAMTIMEID/processed/SCANNAME/reco_~#~#//
--
--Click on one file and click open
--
--You do not need to load any additional dark images.
--
--Skip "Normalize, Minus Log, Rotate" in the Preperation Tab. The optional steps are still optional. (see below)
--
--In principle, you can directly proceed to the third tab "Reconstruction".
--
  \\
--= {{id name="03aReconstructionwithRecoGUI-Preparationofdataforreconstruction"/}}Preparation of data for reconstruction  =
++ Go to "Prep" tab.
--(Can be skipped for Holotomography)
--
--Go to "Prep" tab.
--
  The following is usually required for reconstruction:
  Click "Normalize" button. This will take several minutes.
@@ -130,115 +130,14 @@
  **Finding the correct center of rotation. **
--First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation
++First, you have to find the correct center of rotation. For this, a single slice is reconstructed with different centers of rotation.
--**~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.)
++**Rot center:** For the start, enter half of your image size (1024 for unbinned data, 512 for data with binning 2.)
--**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.
++Delta: Range
--**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)
--
--**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.)
--
--**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.
--
--[[image:attach:image2022-11-14_14-4-49.png||thumbnail="true" height="250"]]
--
--in blue the coordinate of the center of rotation; in yellow the position number of the preview slider
--
--**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.
--
  \\
--How does a good rotation center look like?
--
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--The ghosting effect on the edges is due to sample movement during the scan.
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--**[[image:attach:image2022-11-14_15-28-50.png||height="250"]]**
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--[[image:attach:image2023-1-23_11-39-57.png||height="400"]]
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  \\
--
--\\
--
--**Reconstruction Parameters. **
--
--When you found the correct rotation center, you can continue with the reconstruction.
--
--Enter the final roation center from the above step.
--
--You can select different reconstruction algorithms and filters. Standard is gridrec and shepp.
--
--You can also add ring removal (can take very long!!!!)
--
--Mask: If you like a circular mask around your data, check this box.
--
--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".
--
--\\
--
--When you are happy with your result, press "Reconstruct full stack".
--
-- You can check the data in ImageJ, and if you are not happy, you can also reconstruct with different parameters/ rotation centers.
--
--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.
--
--\\
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@@ -1,1 +1,1 @@
--365845773
++236815113

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@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/P5I/pages/365845773/03a Reconstruction with Reco GUI
++https://confluence.desy.de/spaces/P5I/pages/236815113/03a Reconstruction with Reco GUI

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