---
title: "Getting Started with dicomtk"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting Started with dicomtk}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

## Overview

`dicomtk` is a self-contained, tidyverse-compliant R interface to the OFFIS **DICOM Toolkit (DCMTK 3.7.1)** with native C++17 / `Rcpp` bindings, `ggplot2` / `Shiny` / 3D volume visualization, PACS networking, and local/cloud LLM integration (`Ollama`, `OpenAI`, `Anthropic Claude`).

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

# Verify bundled DCMTK 3.7.1 engine & dictionary
dicom_info()
```

## Reading DICOM Headers & Tidyverse Workflows

```{r read-header}
dcm_file <- system.file("extdata", "example.dcm", package = "dicomtk")

# Long tidy tibble of DICOM elements
hdr <- read_dicom(dcm_file)
hdr |>
  filter(group %in% c("0008", "0028")) |>
  select(tag, vr, keyword, name, value) |>
  head(10)

# Wide format (1 row per file, columns named by DICOM keyword)
read_dicom(dcm_file, wide = TRUE) |>
  select(any_of(c("file", "Modality", "Rows", "Columns", "BitsAllocated")))
```

## Visualizing DICOM Images (`ggplot2`, Clinical Windows, and 3D MPR/MIP)

```{r plot-dicom, fig.width = 5, fig.height = 5}
plot_dicom(dcm_file, window = "auto", palette = "gray", title = "Example DICOM Slice")
```

## Anonymization & Tag Modification

```{r anonymize}
anon_path <- dicom_anonymize(
  dcm_file,
  patient_name = "STUDY^SUBJECT01",
  patient_id = "SUBJ001",
  shift_days = -365
)
dicom_tag_value(anon_path, c("PatientName", "PatientID", "PatientIdentityRemoved"))
```

## AI / LLM Integration (Ollama, OpenAI, and Anthropic Claude)

```{r llm-demo}
# Configure local Ollama or OpenAI/Anthropic provider
# ollama_llm <- dicom_llm("ollama", model = "llava:13b")
# openai_llm <- dicom_llm("openai", model = "gpt-4o")
# claude_llm <- dicom_llm("anthropic", model = "claude-sonnet-4-20250514")

# Deterministic local mode for offline reproducibility
local_ai <- dicom_llm("offline")
dicom_summarize(dcm_file, llm = local_ai)
dicom_report(dcm_file, llm = local_ai)
```