RIA (version 1.6.1)

geometry: Calculates geometry-based parameters of RIA image

Description

Calculates geometry-based parameters of original or subcomponents of an image after discretization. By default the $modif image will be used to calculate statistics. If use_slot is given, then the data present in RIA_image$use_slot will be used for calculations. Results will be saved into the stat_geometry slot. The name of the subslot is determined by the supplied string in save_name, or is automatically generated by RIA.

Usage

geometry(
  RIA_data_in,
  xy_dim = RIA_data_in$log$orig_xy_dim,
  z_dim = RIA_data_in$log$orig_z_dim,
  all_vol = RIA_data_in$log$orig_vol_mm,
  all_surf = RIA_data_in$log$orig_surf_mm,
  calc_dist = FALSE,
  calc_sub = TRUE,
  use_type = "single",
  use_orig = FALSE,
  use_slot = NULL,
  save_name = NULL,
  verbose_in = TRUE
)

Value

RIA_image containing geometry calculations.

Arguments

RIA_data_in

RIA_image.

xy_dim

numeric, in plane resolution.

z_dim

numeric, cross plane resolution.

all_vol

numeric, volume of whole lesion.

all_surf

numeric, surface of whole lesion.

calc_dist

logical, whether to calculate distances, may take very long.

calc_sub

logical, indicating whether to calculate metrics for all different values present in the image. This can be useful for calculating metrics of subcomponents for a discretized image. If FALSE, then all voxels are treated equally and the results will be based on the whole image.

use_type

string, can be "single" which runs the function on a single image, which is determined using "use_orig" or "use_slot". "discretized" takes all datasets in the RIA_image$discretized slot and runs the analysis on them.

use_orig

logical, indicating to use image present in RIA_data$orig. If FALSE, the modified image will be used stored in RIA_data$modif.

use_slot

string, name of slot where data wished to be used is. Use if the desired image is not in the data$orig or data$modif slot of the RIA_image. For example, if the desired dataset is in RIA_image$discretized$ep_4, then use_slot should be discretized$ep_4. The results are automatically saved. If the results are not saved to the desired slot, then please use save_name parameter.

save_name

string, indicating the name of subslot of $stat_geometry to save results to. If left empty, then it will be automatically determined by RIA.

verbose_in

logical indicating whether to print detailed information. Most prints can also be suppressed using the suppressMessages function.

References

Márton KOLOSSVÁRY et al. Radiomic Features Are Superior to Conventional Quantitative Computed Tomographic Metrics to Identify Coronary Plaques With Napkin-Ring Sign Circulation: Cardiovascular Imaging (2017). DOI: 10.1161/circimaging.117.006843 https://pubmed.ncbi.nlm.nih.gov/29233836/

Márton KOLOSSVÁRY et al. Cardiac Computed Tomography Radiomics: A Comprehensive Review on Radiomic Techniques. Journal of Thoracic Imaging (2018). DOI: 10.1097/RTI.0000000000000268 https://pubmed.ncbi.nlm.nih.gov/28346329/

Examples

if (FALSE) {
#Calculate geometry-based parameters on original image
RIA_image <- geometry(RIA_image, use_orig = TRUE, calc_sub = FALSE)

#Discretize loaded image and then calculate geometry-based statistics on subcomponents
RIA_image <- discretize(RIA_image, bins_in = c(4,8), equal_prob = TRUE, use_orig = TRUE)
RIA_image <- geometry(RIA_image, use_orig = FALSE, calc_sub = TRUE)

#Use use_slot parameter to set which image to use
RIA_image <- geometry(RIA_image, use_orig = FALSE, calc_sub = TRUE, use_slot = "discretized$ep_4")

#Batch calculation of geometry-based statistics on all discretized images and subcomponents
RIA_image <- geometry(RIA_image, use_type = "discretized", calc_sub = TRUE)
}