---
title: "DICOM Image Visualization: ggplot2, Clinical Windows, Shiny, and 3D Volumes"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{DICOM Image Visualization: ggplot2, Clinical Windows, Shiny, and 3D Volumes}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Overview

`dicomtk` provides a complete medical image visualization pipeline built on native C++17 pixel extraction (`read_dicom_pixels()`), VOI LUT window/level presets (`dicom_window()`), composable `ggplot2` rendering (`plot_dicom()` / `ggdicom()`), an interactive `Shiny` viewer (`dicom_viewer()`), and 3D volumetric rendering (`render_volume()`).

```{r setup}
library(dicomtk)
library(ggplot2)

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

## Extracting Pixel Data & Applying Clinical Window Presets

`read_dicom_pixels()` decodes 8-bit, 16-bit, or 32-bit monochrome and RGB pixel streams (including RLE-compressed frames) and applies Modality LUT rescaling (`RescaleSlope` and `RescaleIntercept`):

```{r 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)
```

## Composable `ggplot2` Rendering (`plot_dicom()` & `ggdicom()`)

```{r 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")
```

## 3D Volumetric Multi-Planar Reconstruction (MPR) & Maximum Intensity Projection (MIP)

```{r 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")
```

## Interactive Shiny Viewer

In an interactive R session, call `dicom_viewer()` to launch a full multi-slice DICOM workstation in your browser or IDE viewer pane:

```r
if (interactive()) {
  dicom_viewer(dcm_file)
}
```