Tomography Recon GUI Training

In this training we will work through a workflow for reconstructing some example data (courtesy of Alison Davenport and her group). The workflow shown here is not the only way of working, and the system is deliberately flexible to allow you to try different things. The data we will be investigating is a pin which is being corroded, all of the interesting science is happening at the tip of this pin, so that is where we will focus on in this example.

1. Starting Dawn
   1. Open a terminal and type
   2. module load dawn/1.10
   3. dawn
2. Opening the Tomography reconstruction Perspective
   1. In Dawn click on the following menu item
   2. Window->Open Perspective->Other->Tomo Recon
   3. The Tomography Reconstruction perspective should now be shown.
3. Adding the data which is to be reconstructed
   1. In the Nexus Navigator, click the NX icon (Purple icon with "Open Nxs" as tool tip)
   2. Browse to "/dls/mx-scratch/tomo/2013/cm12345-1/13429_subx.nxs"
   3. Click finish, the entry should be now available in the NeXus Navigator
   4. Normally a whole directory of files could be added in this step so you wouldn't need to do it for every file, but in this example we just pick one.
4. Selecting the data which will be reconstructed
   1. In the Nexus Navigator view, click once on 13429_subx.nxs, the process takes a second or so to kick off so don't panic if nothing happens immediately
   2. Wait for all items in the Progress view to disappear
   3. You should now see a projection from your chosen dataset in the Projections view
5. Creating a preview reconstruction
   1. In the Parameters View, click the Preview Recon button
   2. Wait for all items in the Progress view to disappear
   3. The Plot 1 view should now show a slice of the reconstruction.
6. Selecting the best slice to look at
   1. In the Projections view, move the mouse over the image, and position the red line at the top of the lighter region which is visible (This is the top of the pin), and then click.
   2. This should now show a different slice of the reconstruction, only a subsample of slices is available, so the line may move,
   3. You can move up and down the stack by dragging the red line, or by using the Prev (Previous) and Next buttons, and this will update in the main view (Plot 1), be aware though that each image is about 60MB in size, and can take a while to update.
   4. Finally put the slice back at the top of the pin, as this is where we are interested.
7. Selecting a Region of Interest
   1. To make things quicker, selecting a region of interest is useful, in the Parameters view click the Define ROI button.
   2. Select the approximate region (1000,1000) to (3000,3000) which is where the sample is, and click OK
   3. The plot should update with only the selected ROI after processing is complete.
8. Finding the best centre of rotation
   1. The current centre of rotation is very bad which is why the image appears blurred, in the Parameters View, click the Find Centre button, this will display the Centre of Rotation view
   2. We know the centre of rotation is about 2000 from the experimental setup, so enter this into the current centre of rotation box, and click the Coarse button
   3. This will scan coarsely around your current centre of rotation so you can see if there is a better one about.
   4. Wait for all the processing in the Progress view to be completed.
   5. Now use the slider to try different centers of rotation, and look at the image as it updates, it can be easier to make the task run in the background so it does not obscure your view. You should see that the least artifacts are visible at 2020, or point 7. Also once a frame is loaded it is cached, so going back to it will be quicker, to make close changes easier to see
   6. With the 2020 image selected now refine your position using the Fine button,
   7. Repeat the process using the slider to find the spot with the least artifacts, it may be useful to zoom in on the plot on the left hand edge of the visible circle whilst doing this, the best spot should be about 2020 still.
   8. Repeat the process with the Very Fine button, and the best centre should be found at about 2019.8 but it is a little subjective at this point.
   9. Now you are happy with the centre of rotation, click the Use This button, and wait for a new reconstruction stack to appear.
9. Select a new ROI
   1. We can now select a more appropriate ROI, so first reset so we can see the whole stack again. To do this click the Reset link in the ROI section of the Parameters view, and wait for the update to complete.
   2. Now click Define ROI again, and select only the region around the pin. Then click OK and wait for the update.
10. Select the best ring artifact removal
    1. We should now select the best ring artifact removal parameters for this system, this is set in the 'Ring Artifacts' section of the Parameters view. Change the value for "High Aspect Ratio Compensation" to 2.0
    2. Now press the Preview Recon button to view the result of this change, the ring artifacts should appear smoothed out a bit more.
11. Reconstruct the whole volume
    1. Now we are happy with the preview reconstruction, we can reconstruct the whole volume using the Full Reconstruction Button at the bottom of the Parameters view.
    2. Once this is clicked, a selection can be made about how much you want to reconstruct of the volume, in this case all the useful data is between 900 and 1300, so set the region to this area, then click Run Reconstruction
    3. You will now see an entry in the Recon Results view at the bottom left of the perspective, you can now move on to something else, but in this tutorial we will wait for the processing to complete, it should only take a few minutes.
12. Visualize the reconstruction
    1. Once the reconstruction has finished, you can double click on the item in Recon Results, which will open the results in the DExplore Perspective.
    2. In the Editor (this is in the middle with a tab which should say something similar to recon_12345.tiff, click the Image Stack item to select the whole stack of images.
    3. Now in the Section below the editor, expand the Dataset Slicing section, and by dragging the dim:1 slider you can visualize your stack of data.
    4. Be aware it may take a while as there is a lot of data on disk, at this point you can use any of the standard DAWN tools to make the visualization easier.