## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(dicomtk)
library(ggplot2)

dcm_file <- system.file("extdata", "example.dcm", package = "dicomtk")

## ----pixels-------------------------------------------------------------------
px <- read_dicom_pixels(dcm_file)
dim(px)

# Apply clinical window presets ("auto", "brain", "stroke", "subdural",
# "lung", "mediastinum", "abdomen", "liver", "bone", "angio")
win_brain <- dicom_window(px, preset = "brain")
range(win_brain)

## ----ggplot-render, fig.width = 5, fig.height = 5-----------------------------
plot_dicom(dcm_file, window = "auto", palette = "gray", title = "Radiological Grayscale")

# Add custom ggplot2 annotations on top of ggdicom()
ggdicom(dcm_file, palette = "inferno", annotate = FALSE) +
  labs(title = "Inferno Colormap with Custom ggplot2 Layer")

## ----volume-render, fig.width = 7, fig.height = 3-----------------------------
series <- read_dicom_series(c(dcm_file, dcm_file, dcm_file))
series

# 3-Plane Orthogonal MPR
render_volume(series, method = "mpr")

# 3-Plane Maximum Intensity Projection (MIP)
render_volume(series, method = "mip", palette = "viridis")