User manuals MuhRec BBlogNorm - neutronimaging/imagingsuite GitHub Wiki

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The BBLogNorm module implements the normalization of projection data to reference images, including open beam, dark current and images with black bodies (BB). The full normalization operation is computed using:

where background images (BG) are computed from BB images (background image computed from open beam images with BBs: , background image computed from sample image with BBs: ) and compensate for scattered neutrons from the sample and the experimental setup. BB images are expected to be acquired without the sample (open beam images with BB) and with the sample (sample images with BB). Several options for this module are available and can be configured through the module dialog. In the first tab of the dialog (Figure 1), the following parameters can be set:

Figure 1: First tab of the configuration dialog for the BBLogNorm module.

  • Averaging method allows to choose between different averaging method to be applied to a stack of dark current, open beam and eventually BB images.
    Methods available: ImageWeightedAverage, ImageAverage, ImageMedian, ImageMax, ImageMin, ImageSum Default value: ImageWeightedAverage
  • Referencing method triggers the execution of the -log.
    Methods available: LogNorm, Norm
    Default value: LogNorm
  • BB option allows to choose different referencing options depending on the type of BB images. Options available:
    • noBB: to be used when no BB images are available or needed. In this case no other parameters need to be configured and the referencing method is the same as the one available in the FullLogNorm module.
    • Interpolate: to be used when the BB images with the sample are acquired at regular angular step. In this case further configuration is done in the second tab "BB images" of the dialog.
    • Average: to be used when a stack of BB images with the sample is taken at the same angular position. In this case the averaging method chosen will be applied and further configuration is done in the second tab "BB images" of the dialog.
    • OneToOne: to be used when the BB images are acquired at the sample angular position of the projection data. It is required that the number of BB images is the same of the projections. Further configuration is done in the second tab of the dialog.
    • ExternalBB: to be used when the background images are created elsewhere. In this case the second part of the tab is activated and it is possible to load such images. Images are expected to be already dose corrected, in the case of the open beam image with BB a single file is expected to be loaded. In the case of the sample image with BBs, the number of images is expected to be equal to the number of projection data, meaning that a one by one correspondence is expected.
      Default value: Interpolate

In the second tab of the dialog, BB images can be loaded and parameters set (Figure2). \

Figure 2: Second tab of the configuration dialog for the BBLogNorm module.

For the open beam with BB images:

  1. Get the file name through the browse button.
  2. On the Open beam with BBs panel, select a ROI including all BBs, or relavant BBs, then click on GetBBroi. On this roi, Otsu thresholding segmentation is applied to detect BB position. In case of the presence of the rotary table it is probably better to exclude it from the roi. From the segmented image a submask is created, defined as circles of a certain radius centered in the weighted center of mass of each BB (this is not always in the center of BB, also due to beam characteristics). The values of the BB images under these points are used to create an interpolated image of the background.
  3. In case the Otsu thresholding fails, there is the option to set manually a threshold value (fraction value between 0.0 and 1.0)
  4. Select the radius for the mask computation. Default value is 2 pixels. Maximum size is defined by the size of the BBs, any radius that defines circle bigger than the maximum size will produce masks of the size of BBs.
  5. Choose the interpolation order along x and y. Options are: ZeroOrder, FirstOrder and SecondOrder. Default value is SecondOrder for both direction. For PSI experiments, higher order for x than the order of y is possibly needed.
  6. Click on the "Compute error" button. This will display the BB mask, obtained by segmenting the BB roi with the defined radius, and the root mean square error for the given interpolation scheme. At this point it can be useful to tune the radius and the interpolation orders to minimize the interpolation error.
  7. If the interpolation error is high, it can be considered to switch from Polynomial to ThinPlateSplines interpolation error (requires longer computational time).

For the sample images with BBs:

  1. Get the file name throw the Browse button.
  2. For the Interpolate BBOption: type the first and last angles. In the OneToOne BBOption, Count must be equal to the number of projection data.
  3. Into the Sample image with BBs panel, select an open beam ROI, then click on GetBBdose.

Click finally on OK, to save all parameters.
Two hidden boolean and one numerical parameters can be finally tuned from the processing tab of the main window:

  • SameMask: if true, the mask is computed only once on the open beam image with BB. The same mask is then used to compute background images from sample images with BBs. This requires that the BBs are in the same position in open beam and sample images with BBs. If false, the mask is computed once again on the first image with sample and BBs and this second mask is used for all sample images with BBs. This option might be used when the BBs in the open beam and sample image are not in the same position, however it requires that the same angular position is available for the first projection image and the first sample image with BBs and that the sample position between the two is the same. Default value: true.
  • tau: mean transmission pattern. It is a parameter which contributes in the computation of background images and can be changed in order to obtain more flat profiles and empty regions closed to zero by lowering its value. This value estimate the decrease in transmission due the presence of the BBs and the holding frame. Default value = 0.97, estimated for the PSI midi setup.
  • PBvariante triggers the use of the proposed formula (true) or a previous simplified one (false), to be use for testing purpose. Default value: true.

Object file: libStdPreprocModules.so

Reference

P. Boillat, C. Carminati, F. Schmid, C. Grünzweig, J. Hovind, A. Kaestner, D. Mannes, M. Morgano, M. Siegwart, P. Trtik, P. Vontobel, and E.H. Lehmann, "Chasing quantitative biases in neutron imaging with scintillator-camera detectors: a practical method with black body grids," Opt. Express 26, 15769-15784 (2018) https://doi.org/10.1364/OE.26.015769

Carminati C, Boillat P, Schmid F, et al. Implementation and assessment of the black body bias correction in quantitative neutron imaging. PLoS ONE. 2019;14(01):1-24. https://doi.org/10.1371/journal.pone.0210300.

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