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Process Images in Folder

Source: R/process_images.R
process_images.Rd

This function processes images in a specified folder, applying various transformations and analyses.

Usage

process_images(
  folder,
  subfolder = FALSE,
  threshold = NULL,
  wavelets = TRUE,
  ef = TRUE,
  testing = TRUE,
  pseudolandmarks = "both",
  save = TRUE,
  pixels_per_mm = NULL,
  detect_scale = FALSE,
  blur_size = 31,
  blur_sigma = 9,
  min_points = 200,
  min_area = 5000,
  n_harmonics = 32,
  n_points = 512,
  scale_mm = 1
)

Arguments

folder

A string specifying the path to the folder containing images.

subfolder

A logical value indicating whether the folder has subfolders.

threshold

A numeric value for binarization. If not provided, the Otsu method is used.

wavelets

A logical value indicating whether to obtain wavelets. Default is TRUE.

ef

A logical value indicating whether to obtain elliptic Fourier descriptors. Default is TRUE.

testing

A logical value indicating whether to save test images. Default is TRUE.

pseudolandmarks

A string specifying the type of pseudolandmarks. Options are 'curvilinear', 'polar', 'both'. Default is 'both'.

save

A logical value indicating whether to save the results as CSV files. Default is TRUE.

pixels_per_mm

A numeric value specifying the scale (pixels per mm). Default is NULL.

detect_scale

A logical value indicating whether to automatically detect the scale bar in the image. Default is FALSE.

blur_size

Size of the Gaussian brush for smoothing (default: 31).

blur_sigma

Sigma of the Gaussian brush for smoothing (default: 9).

min_points

Minimum number of points required for a valid contour (default: 200).

min_area

Minimum area required for a valid contour (default: 5000).

n_harmonics

Number of elliptic Fourier harmonics to calculate (default: 32).

n_points

Target number of points for resampling (default: 512).

scale_mm

Total length in mm of the scale bar for detection (default: 1).

Value

Invisible NULL. The function is used for its side effects (creating files).

Details

The function generates the following files in the `Polar` (and `Cartesian`) directories:

  • MorphometricsEN.csv: Table with shape indices (Area, Perimeter, Circularity, etc.).

  • DistanciaEN.csv and Distancia_NormEN.csv: Raw and normalized distances (radii or perimeter).

  • Wavelet_xEN.csv: Wavelet coefficients for scales 1 to 9.

  • EllipticCoeEN.csv: Elliptic Fourier coefficients (if ef = TRUE).

  • Coords.csv: Contour coordinates.

If testing = TRUE, diagnostic images are also saved:

  • zonal_[ImageName].jpg: Visualization of the contour and analysis sectors.

  • wavelet_[ImageName].jpg: Visualization of the wavelet transform.

Examples

if (FALSE) { # \dontrun{
# Process all images in the "images" folder
process_images(folder = "path/to/images", pixels_per_mm = 100)
} # }