Usage

SCOPE-XR provides two main interfaces designed for different user workflows.

The program supports configurable execution via YAML configuration files. You can find an example of these files in the examples folder, along with some simulated images to test the package.

Supported Image Formats

The supported input image formats are:

• .png

• .tif / .tiff

• .raw (must be accompanied by a corresponding .xml metadata file)

• .dcm (DICOM)

GUI Execution

The recommended way for routine analysis. It features live image previews and interactive parameter tuning. To run the GUI, simply type:

scopexr-gui

GUI Features:

• Easy Mode Selection: Separate tabs for “Focal Spot (FS)” and “PSF” analysis.

• Automatic Configuration: The GUI automatically loads all default parameters from fs_args.yaml or psf_args.yaml on startup.

• Image Preview: Load .png, .tif/.tiff, or .dcm images to see a preview directly in the app.

• Full Parameter Control: All CLI flags are editable via interactive widgets.

• Edit Config Files: A button allows you to directly open and edit the default .yaml config file for the active tab.

• Live Output: All console output from the analysis script is printed directly to a text box within the GUI.

CLI Execution

Ideal for batch processing and integration into automated research pipelines. To run the program with the default settings (as defined in fs_args.yaml or psf_args.yaml), use the following commands:

• Focal Spot:

  scopexr-fs --f "path/to/img.png"
  

• PSF:

  scopexr-psf --f "path/to/img.png"
  

Use the --help flag with any command to see all available parameters.

Overriding Configuration Parameters

You can override any configuration value directly from the command line by adding the corresponding flag. For example:

scopexr-fs --f "path/to/img.png" --p 0.2

Available CLI Flags

Focal Spot CLI

Flag	Description
--config (str)	Path to the YAML configuration file.
--f (str)	Required. Path to the input image file (.raw, .png, .tif/.tiff, .dcm).
--o (str)	Output directory to store results.
--p (float)	Pixel size in mm.
--d (float)	Physical diameter of the circular object in mm.
--no_hough	Skip Hough Transform for automatic circle detection.
--m (float)	Image magnification. If not provided, estimated automatically.
--n (int)	Minimum number of pixels required to achieve a reasonable focal spot size.
--nangles (int)	Number of angular projections for profile extraction.
--hl (int)	Half length of the extracted radial profiles.
--ds (int)	Step size used for numerical derivative calculations.
--axis_shifts (int)	Number of steps to shift the sinogram axis.
--filter (str)	Filter used. Options: ramp, shepp-logan, cosine, hamming, hann. Use None for no filter.
--avg_number (int)	Number of profiles to average (must be odd). Only used if --avg is true.
--sym	Symmetrize the sinogram before reconstruction.
--shift	Enable automatic sinogram shifting.
--no_shift	Disable automatic sinogram shifting. (Mutually exclusive with --shift)
--avg	Average neighboring sinogram profiles to improve FWHM estimation.
--no_avg	Do not average neighboring profiles. (Mutually exclusive with --avg)
--show	Display plots during processing (matplotlib windows).

PSF CLI

Flag	Description
--config (str)	Path to the YAML configuration file.
--f (str)	Required. Path to the input image file (.raw, .png, .tif/.tiff, .dcm).
--o (str)	Output directory to store results.
--p (float)	Pixel size in mm.
--d (float)	Physical diameter of the circular object in mm.
--no_hough	Skip Hough Transform for automatic circle detection.
--nangles (int)	Number of angular projections for profile extraction.
--hl (int)	Half length of the extracted radial profiles.
--ds (int)	Step size used for numerical derivative calculations.
--axis_shifts (int)	Number of steps to shift the sinogram axis.
--filter (str)	Filter used. Options: ramp, shepp-logan, cosine, hamming, hann. Use None for no filter.
--avg_number (int)	Number of profiles to average (must be odd). Only used if --avg is true.
--sym	Symmetrize the sinogram before reconstruction.
--dtheta (float)	Angle of the circular sector for oversampling (in degrees).
--resample2 (int)	Radial sampling density for the coarse grid when oversampling is enabled.
--gaussian_sigma	Controls oversampling mode: 0/None uses direct binned statistics; >0 applies fine-grid resample + Gaussian blur before coarse binning.
--shift	Enable automatic sinogram shifting.
--no_shift	Disable automatic sinogram shifting. (Mutually exclusive with --shift)
--avg	Average neighboring sinogram profiles to improve FWHM estimation.
--no_avg	Do not average neighboring profiles. (Mutually exclusive with --avg)
--oversample	Perform oversampling.
--no_oversample	Disable oversampling. (Mutually exclusive with --oversample)
--show	Display plots during processing (matplotlib windows).