Oury Monchi

17 papers B 1Journal 14Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
npj Digit. Medicine
Raissa Souza, Emma A. M. Stanley, Anthony J. Winder, Chris Kang, Kimberly Amador, Erik Y. Ohara, Gabrielle Dagasso, Richard Camicioli, Oury Monchi, Zahinoor Ismail, Matthias Wilms, Nils D. Forkert
2024 J jnl
Frontiers Artif. Intell.
Raissa Souza, Emma A. M. Stanley, Milton Camacho, Richard Camicioli, Oury Monchi, Zahinoor Ismail, Matthias Wilms, Nils D. Forkert
2024 conf
FAIMI/EPIMI@MICCAI
Raissa Souza, Emma A. M. Stanley, Richard Camicioli, Oury Monchi, Zahinoor Ismail, Matthias Wilms, Nils D. Forkert
2024 J jnl
IEEE J. Biomed. Health Informatics
Raissa Souza, Anthony J. Winder, Emma A. M. Stanley, Vibujithan Vigneshwaran, Milton Camacho, Richard Camicioli, Oury Monchi, Matthias Wilms, Nils D. Forkert
2023 J jnl
J. Am. Medical Informatics Assoc.
Raissa Souza, Matthias Wilms, Milton Camacho, G. Bruce Pike, Richard Camicioli, Oury Monchi, Nils D. Forkert
2020 J jnl
IEEE Trans. Biomed. Eng.
Stefan T. Lang, Liu Shi Gan, Cael McLennan, Oury Monchi, John J. P. Kelly
2012 J jnl
NeuroImage
Maxime Montembeault, Sven Joubert, Julien Doyon, Julie Carrier, Jean-François Gagnon, Oury Monchi, Ovidiu V. Lungu, Sylvie Belleville, Simona Maria Brambati
2011 J jnl
NeuroImage
Thomas Jubault, Jean-François Gagnon, Sherif Karama, Alain Ptito, Anne-Louise Lafontaine, Alan C. Evans, Oury Monchi
2009 J jnl
NeuroImage
Ji Hyun Ko, Alain Ptito, Oury Monchi, Sang Soo Cho, Thilo Van Eimeren, Giovanna Pellecchia, Bénédicte Ballanger, Pablo Rusjan, Sylvain Houle, Antonio P. Strafella
2008 J jnl
Int. J. Biomed. Imaging
Oury Monchi, Habib Benali, Julien Doyon, Antonio P. Strafella
2008 J jnl
Int. J. Biomed. Imaging
Ji Hyun Ko, Oury Monchi, Alain Ptito, Michael Petrides, Antonio P. Strafella
2006 J jnl
NeuroImage
Oury Monchi, Ji Hyun Ko, Antonio P. Strafella
2006 J jnl
NeuroImage
Antonio P. Strafella, Ji Hyun Ko, Oury Monchi
2005 B conf
IJCNN
Oury Monchi
2000 J jnl
Neural Networks
Oury Monchi, John G. Taylor, Alain Dagher
1999 J jnl
Inf. Sci.
Oury Monchi, John G. Taylor
1997 conf
NCPW
Oury Monchi, John G. Taylor
src/main.rs
← Index src/main.rs rust
mod highlight;

use std::collections::BTreeMap;
use std::fs;
use std::io::Read;
use std::path::{Path, PathBuf};
use std::time::Instant;

use walkdir::WalkDir;

use highlight::highlight_code;

/// Above this threshold the file is read in full and classified
/// (text or binary) based on its complete content.
const FULL_READ_LIMIT: u64 = 4_000_000; // 4 MB
/// For files larger than the threshold above, we only read a preview
/// of this size (so we never load huge files fully into memory).
const PREVIEW_BYTES: usize = 16_384;
/// How many bytes of binary content to show in the hex dump.
const HEXDUMP_BYTES: usize = 4096;

struct FileResult {
    rel_path: PathBuf, // relative path of the original file
    out_rel: PathBuf,  // relative path of the generated .html file (inside out/)
    label: String,     // label shown in the badge (language, or "binary")
}

enum Unreadable {
    IoError(PathBuf),
}

enum Content {
    /// Successfully decoded text. `truncated` indicates whether the file
    /// is larger than what was actually read (very large files: preview only).
    Text { content: String, truncated: bool, total_size: u64 },
    /// Content that isn't valid UTF-8 text: we show a hex dump instead
    /// of trying to decode it.
    Binary { preview: Vec<u8>, total_size: u64, truncated: bool },
}

/// Reads a file safely: for small files, reads everything and classifies
/// text/binary based on the full content; for large files, reads only a
/// prefix, to avoid loading huge files into memory.
fn read_content(path: &Path, total_size: u64) -> std::io::Result<Content> {
    if total_size <= FULL_READ_LIMIT {
        let bytes = fs::read(path)?;
        match String::from_utf8(bytes) {
            Ok(s) => Ok(Content::Text {
                content: s,
                truncated: false,
                total_size,
            }),
            Err(e) => Ok(Content::Binary {
                preview: e.into_bytes(),
                total_size,
                truncated: false,
            }),
        }
    } else {
        let mut f = fs::File::open(path)?;
        let mut buf = vec![0u8; PREVIEW_BYTES];
        let n = f.read(&mut buf)?;
        buf.truncate(n);

        match std::str::from_utf8(&buf) {
            Ok(s) => Ok(Content::Text {
                content: s.to_string(),
                truncated: true,
                total_size,
            }),
            Err(e) => {
                let valid_up_to = e.valid_up_to();
                // If the error is only due to cutting a multi-byte
                // character in half (common when reading an arbitrary
                // prefix of a text file), still treat it as text.
                if valid_up_to > 0 && buf.len() - valid_up_to <= 4 {
                    let s = std::str::from_utf8(&buf[..valid_up_to]).unwrap().to_string();
                    Ok(Content::Text {
                        content: s,
                        truncated: true,
                        total_size,
                    })
                } else {
                    Ok(Content::Binary {
                        preview: buf,
                        total_size,
                        truncated: true,
                    })
                }
            }
        }
    }
}

/// Tree node used to build the index (index.html)
#[derive(Default)]
struct Node {
    dirs: BTreeMap<String, Node>,
    files: Vec<(String, String, PathBuf)>, // (display_name, label, href relative to the index)
}

impl Node {
    fn insert_file(&mut self, components: &[String], display_name: String, label: String, href: PathBuf) {
        if components.is_empty() {
            self.files.push((display_name, label, href));
        } else {
            let head = &components[0];
            let child = self.dirs.entry(head.clone()).or_default();
            child.insert_file(&components[1..], display_name, label, href);
        }
    }

    fn render(&self, out: &mut String) {
        out.push_str("<ul class=\"tree\">\n");
        for (name, node) in &self.dirs {
            out.push_str(&format!(
                "<li class=\"dir\"><span class=\"dir-name\">\u{1F4C1} {}</span>\n",
                escape_html(name)
            ));
            node.render(out);
            out.push_str("</li>\n");
        }
        for (name, label, href) in &self.files {
            out.push_str(&format!(
                "<li class=\"file\"><a href=\"{}\">\u{1F4C4} {}</a> <span class=\"badge\">{}</span></li>\n",
                href.to_string_lossy().replace('\\', "/"),
                escape_html(name),
                escape_html(label)
            ));
        }
        out.push_str("</ul>\n");
    }
}

fn main() {
    let args: Vec<String> = std::env::args().collect();
    let input_dir = args.get(1).cloned().unwrap_or_else(|| ".".to_string());
    let output_dir = args.get(2).cloned().unwrap_or_else(|| "out".to_string());
    // Extra directory names to exclude, optional, comma-separated
    // (e.g. "node_modules,.git"). Nothing is excluded by default:
    // the generator includes everything it finds, including
    // __pycache__, compiled files, binaries, etc.
    let extra_excludes: Vec<String> = args
        .get(3)
        .map(|s| s.split(',').map(|p| p.trim().to_string()).filter(|p| !p.is_empty()).collect())
        .unwrap_or_default();

    let input = PathBuf::from(&input_dir);
    let output = PathBuf::from(&output_dir);

    if !input.is_dir() {
        eprintln!("Error: '{}' is not a valid directory.", input.display());
        std::process::exit(1);
    }

    if let Err(e) = fs::create_dir_all(&output) {
        eprintln!("Error creating the output directory: {e}");
        std::process::exit(1);
    }

    // Absolute path of the output directory, so we can exclude it from the
    // scan in case it's nested inside the input directory (e.g. input=".",
    // output="out"). This is the only automatic exclusion and it can't be
    // turned off: it only prevents the program from processing the files
    // it is currently writing.
    let output_abs = fs::canonicalize(&output).unwrap_or_else(|_| output.clone());

    println!("Scanning '{}' -> '{}'", input.display(), output.display());
    if !extra_excludes.is_empty() {
        println!("Directories excluded on request: {}", extra_excludes.join(", "));
    }
    let start = Instant::now();

    let mut results: Vec<FileResult> = Vec::new();
    let mut unreadable: Vec<Unreadable> = Vec::new();
    let mut n_binary = 0usize;
    let mut n_truncated = 0usize;

    for entry in WalkDir::new(&input)
        .into_iter()
        .filter_entry(|e| {
            if e.file_type().is_dir() {
                if let Some(name) = e.file_name().to_str() {
                    if extra_excludes.iter().any(|x| x == name) {
                        return false;
                    }
                }
                if let Ok(abs) = fs::canonicalize(e.path()) {
                    if abs == output_abs {
                        return false;
                    }
                }
            }
            true
        })
    {
        let entry = match entry {
            Ok(e) => e,
            Err(_) => continue,
        };

        if !entry.file_type().is_file() {
            continue;
        }

        let path = entry.path();
        let rel_path = match path.strip_prefix(&input) {
            Ok(p) => p.to_path_buf(),
            Err(_) => path.to_path_buf(),
        };

        let meta = match fs::metadata(path) {
            Ok(m) => m,
            Err(_) => {
                unreadable.push(Unreadable::IoError(rel_path));
                continue;
            }
        };

        let content = match read_content(path, meta.len()) {
            Ok(c) => c,
            Err(_) => {
                unreadable.push(Unreadable::IoError(rel_path));
                continue;
            }
        };

        let syntax_lang = detect_language(path);

        let (body_html, label, note): (String, String, Option<String>) = match &content {
            Content::Text { content, truncated, total_size } => {
                let body = highlight_code(content, syntax_lang);
                let note = if *truncated {
                    n_truncated += 1;
                    Some(format!(
                        "Truncated preview: showing the first {} bytes out of {} total.",
                        content.len(),
                        total_size
                    ))
                } else {
                    None
                };
                (body, syntax_lang.to_string(), note)
            }
            Content::Binary { preview, total_size, truncated } => {
                n_binary += 1;
                let dump = hex_dump(preview, HEXDUMP_BYTES);
                let shown = preview.len().min(HEXDUMP_BYTES);
                let note = Some(format!(
                    "Binary file: {} bytes total. Showing the first {} bytes as hex.{}",
                    total_size,
                    shown,
                    if *truncated { " (only the first bytes of the file were read)" } else { "" }
                ));
                (escape_html(&dump), "binary".to_string(), note)
            }
        };

        let mut out_rel = rel_path.clone();
        let new_name = format!(
            "{}.html",
            out_rel.file_name().unwrap_or_default().to_string_lossy()
        );
        out_rel.set_file_name(new_name);

        let out_path = output.join(&out_rel);
        if let Some(parent) = out_path.parent() {
            let _ = fs::create_dir_all(parent);
        }

        let depth = out_rel.components().count().saturating_sub(1);
        let back_to_index = "../".repeat(depth);

        let html = render_file_html(
            &rel_path.to_string_lossy(),
            &label,
            &body_html,
            note.as_deref(),
            &back_to_index,
        );

        if fs::write(&out_path, html).is_ok() {
            results.push(FileResult {
                rel_path,
                out_rel,
                label,
            });
        }
    }

    // Build the tree for the index
    let mut root = Node::default();
    for r in &results {
        let components: Vec<String> = r
            .rel_path
            .parent()
            .map(|p| {
                p.components()
                    .map(|c| c.as_os_str().to_string_lossy().to_string())
                    .filter(|s| !s.is_empty())
                    .collect()
            })
            .unwrap_or_default();
        let display_name = r
            .rel_path
            .file_name()
            .unwrap_or_default()
            .to_string_lossy()
            .to_string();
        root.insert_file(
            &components,
            display_name,
            r.label.clone(),
            r.out_rel.clone(),
        );
    }

    let mut tree_html = String::new();
    root.render(&mut tree_html);

    let index_html = render_index_html(&tree_html, results.len(), n_binary, n_truncated);
    let _ = fs::write(output.join("index.html"), index_html);

    let elapsed = start.elapsed();
    println!(
        "Done in {:.2?}: {} files included ({} binary, {} with truncated preview), {} unreadable.",
        elapsed,
        results.len(),
        n_binary,
        n_truncated,
        unreadable.len()
    );
    for u in &unreadable {
        match u {
            Unreadable::IoError(p) => println!("  unreadable (I/O error): {}", p.display()),
        }
    }
    println!("Open {}/index.html in your browser.", output.display());
}

/// Produces a hex dump (in the style of `xxd -C`) of the first `limit` bytes.
fn hex_dump(bytes: &[u8], limit: usize) -> String {
    let show = &bytes[..bytes.len().min(limit)];
    let mut out = String::with_capacity(show.len() * 4);
    for (i, chunk) in show.chunks(16).enumerate() {
        let offset = i * 16;
        out.push_str(&format!("{:08x}  ", offset));
        for (j, b) in chunk.iter().enumerate() {
            out.push_str(&format!("{:02x} ", b));
            if j == 7 {
                out.push(' ');
            }
        }
        let missing = 16usize.saturating_sub(chunk.len());
        for _ in 0..missing {
            out.push_str("   ");
        }
        out.push_str(" |");
        for b in chunk {
            let c = *b;
            if (0x20..0x7f).contains(&c) {
                out.push(c as char);
            } else {
                out.push('.');
            }
        }
        out.push_str("|\n");
    }
    out
}

/// Determines the language (used to pick syntax-highlighting rules)
/// from the file's name/extension. This is only used when the content
/// turns out to actually be text; binary files are classified as such
/// regardless by read_content.
fn detect_language(path: &Path) -> &'static str {
    let file_name = path
        .file_name()
        .map(|s| s.to_string_lossy().to_lowercase())
        .unwrap_or_default();

    match file_name.as_str() {
        "dockerfile" => return "dockerfile",
        "makefile" | "gnumakefile" => return "makefile",
        "cmakelists.txt" => return "cmake",
        ".gitignore" | ".dockerignore" | ".npmignore" => return "plaintext",
        "cargo.toml" | "cargo.lock" => return "ini",
        _ => {}
    }

    let ext = path
        .extension()
        .map(|s| s.to_string_lossy().to_lowercase())
        .unwrap_or_default();

    match ext.as_str() {
        "py" | "pyw" | "pyi" => "python",
        "rs" => "rust",
        "js" | "mjs" | "cjs" => "javascript",
        "jsx" => "javascript",
        "ts" => "typescript",
        "tsx" => "typescript",
        "java" => "java",
        "c" => "c",
        "h" => "c",
        "hpp" | "hh" | "hxx" => "cpp",
        "cpp" | "cc" | "cxx" => "cpp",
        "cs" => "csharp",
        "go" => "go",
        "rb" => "ruby",
        "php" => "php",
        "html" | "htm" => "xml",
        "css" => "css",
        "scss" | "sass" => "scss",
        "less" => "less",
        "json" => "json",
        "xml" => "xml",
        "yaml" | "yml" => "yaml",
        "toml" | "ini" | "cfg" | "conf" => "ini",
        "sh" | "bash" | "zsh" => "bash",
        "sql" => "sql",
        "md" | "markdown" => "markdown",
        "kt" | "kts" => "kotlin",
        "swift" => "swift",
        "lua" => "lua",
        "r" => "r",
        "pl" | "pm" => "perl",
        "groovy" | "gradle" => "groovy",
        "vb" => "vbnet",
        "graphql" | "gql" => "graphql",
        "diff" | "patch" => "diff",
        "bat" | "cmd" => "dos",
        "ps1" => "powershell",
        "vue" => "xml",
        "txt" => "plaintext",
        _ => "plaintext",
    }
}

fn escape_html(s: &str) -> String {
    let mut out = String::with_capacity(s.len());
    for c in s.chars() {
        match c {
            '&' => out.push_str("&amp;"),
            '<' => out.push_str("&lt;"),
            '>' => out.push_str("&gt;"),
            '"' => out.push_str("&quot;"),
            '\'' => out.push_str("&#39;"),
            _ => out.push(c),
        }
    }
    out
}

const STYLE: &str = r#"
:root {
  --bg: #0d1117;
  --panel: #161b22;
  --text: #c9d1d9;
  --muted: #8b949e;
  --accent: #58a6ff;
  --border: #30363d;
}
* { box-sizing: border-box; }
body {
  margin: 0;
  background: var(--bg);
  color: var(--text);
  font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif;
}
header {
  padding: 14px 20px;
  background: var(--panel);
  border-bottom: 1px solid var(--border);
  display: flex;
  align-items: center;
  gap: 12px;
  flex-wrap: wrap;
}
header a { color: var(--accent); text-decoration: none; font-weight: 600; }
header a:hover { text-decoration: underline; }
.path { color: var(--muted); font-size: 0.9em; word-break: break-all; }
.note {
  padding: 10px 20px;
  background: #21262d;
  border-bottom: 1px solid var(--border);
  color: var(--muted);
  font-size: 0.85em;
}
main { padding: 0; }
pre {
  margin: 0;
  padding: 16px 20px 40px 20px;
  overflow-x: auto;
  font-size: 13px;
  line-height: 1.5;
}
code { font-family: "SFMono-Regular", Consolas, "Liberation Mono", Menlo, monospace; }
.container { max-width: 1000px; margin: 30px auto; padding: 0 20px 60px; }
h1 { font-size: 1.6em; }
.meta { color: var(--muted); font-size: 0.9em; margin-bottom: 20px; }
ul.tree { list-style: none; padding-left: 18px; margin: 6px 0; }
ul.tree > li { margin: 4px 0; }
.dir-name { font-weight: 600; color: var(--text); }
.file a { color: var(--accent); text-decoration: none; }
.file a:hover { text-decoration: underline; }
.badge {
  display: inline-block;
  font-size: 0.72em;
  color: var(--muted);
  border: 1px solid var(--border);
  border-radius: 10px;
  padding: 1px 8px;
  margin-left: 6px;
}
.skipped { color: var(--muted); font-size: 0.85em; margin-top: 30px; }

/* Syntax highlighting: generated in Rust, no JavaScript involved. */
.c { color: #8b949e; font-style: italic; }
.s { color: #a5d6ff; }
.n { color: #79c0ff; }
.k { color: #ff7b72; font-weight: 600; }
"#;

fn render_file_html(rel_path: &str, label: &str, body_html: &str, note: Option<&str>, back_to_index: &str) -> String {
    let title = escape_html(rel_path);
    let note_html = match note {
        Some(n) => format!("<div class=\"note\">{}</div>\n", escape_html(n)),
        None => String::new(),
    };
    format!(
        r#"<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>{title}</title>
<style>{STYLE}</style>
</head>
<body>
<header>
  <a href="{back_to_index}index.html">&larr; Index</a>
  <span class="path">{title}</span>
  <span class="badge">{label}</span>
</header>
{note_html}<main>
<pre><code>{body_html}</code></pre>
</main>
</body>
</html>
"#
    )
}

fn render_index_html(tree_html: &str, n_ok: usize, n_binary: usize, n_truncated: usize) -> String {
    let mut extra = String::new();
    if n_binary > 0 {
        extra.push_str(&format!(
            "<p class=\"skipped\">{} binary files included with a hex-dump preview.</p>",
            n_binary
        ));
    }
    if n_truncated > 0 {
        extra.push_str(&format!(
            "<p class=\"skipped\">{} very large files shown as a truncated preview only.</p>",
            n_truncated
        ));
    }

    let folder_emoji = '\u{1F4C2}';
    format!(
        r#"<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Source index</title>
<style>{STYLE}</style>
</head>
<body>
<div class="container">
<h1>{folder_emoji} Source index</h1>
<p class="meta">{n_ok} files included in total.</p>
{tree_html}
{extra}
</div>
</body>
</html>
"#
    )
}