//! FreeSurfer annotation file reading
//!
//! Reads .annot files containing parcellation labels and color tables.
//! Common atlases include:
//! - aparc (Desikan-Killiany atlas)
//! - aparc.a2009s (Destrieux atlas)
//! - aparc.DKTatlas (DKT atlas)

use std::collections::HashMap;
use std::fs::File;
use std::io::{BufReader, Read};
use std::path::Path;

use byteorder::{LittleEndian, ReadBytesExt};
use serde::{Deserialize, Serialize};

use crate::error::{AnatomyError, Result};
use crate::surface::Hemisphere;

/// A color entry in the annotation color table
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct AnnotationEntry {
    /// Region name
    pub name: String,
    /// Red component (0-255)
    pub r: u8,
    /// Green component (0-255)
    pub g: u8,
    /// Blue component (0-255)
    pub b: u8,
    /// Alpha component (0-255, usually 0 = opaque)
    pub a: u8,
}

impl AnnotationEntry {
    /// Get RGB color as [0-1] floats
    pub fn color_rgb(&self) -> [f32; 3] {
        [
            self.r as f32 / 255.0,
            self.g as f32 / 255.0,
            self.b as f32 / 255.0,
        ]
    }

    /// Get RGBA color as [0-1] floats
    pub fn color_rgba(&self) -> [f32; 4] {
        [
            self.r as f32 / 255.0,
            self.g as f32 / 255.0,
            self.b as f32 / 255.0,
            1.0 - (self.a as f32 / 255.0), // FreeSurfer uses 0=opaque
        ]
    }
}

/// Color table mapping label IDs to entries
#[derive(Debug, Clone, Default, Serialize, Deserialize)]
pub struct ColorTable {
    /// Entries indexed by label ID
    pub entries: HashMap<i32, AnnotationEntry>,
}

impl ColorTable {
    /// Get entry by label ID
    pub fn get(&self, label: i32) -> Option<&AnnotationEntry> {
        self.entries.get(&label)
    }

    /// Get all region names
    pub fn region_names(&self) -> Vec<&str> {
        self.entries.values().map(|e| e.name.as_str()).collect()
    }

    /// Number of regions
    pub fn n_regions(&self) -> usize {
        self.entries.len()
    }
}

/// Parcellation annotation for a brain surface
#[derive(Debug, Clone)]
pub struct Annotation {
    /// Per-vertex label IDs (using the packed RGBA format)
    pub labels: Vec<i32>,
    /// Color table with region info
    pub color_table: ColorTable,
    /// Atlas name (e.g., "aparc", "aparc.a2009s")
    pub atlas: String,
    /// Hemisphere
    pub hemisphere: Hemisphere,
}

impl Annotation {
    /// Number of vertices
    pub fn n_vertices(&self) -> usize {
        self.labels.len()
    }

    /// Get the region name for a vertex
    pub fn vertex_region(&self, vertex: usize) -> Option<&str> {
        let label = self.labels.get(vertex)?;
        self.color_table.get(*label).map(|e| e.name.as_str())
    }

    /// Get the color for a vertex
    pub fn vertex_color(&self, vertex: usize) -> Option<[f32; 3]> {
        let label = self.labels.get(vertex)?;
        self.color_table.get(*label).map(AnnotationEntry::color_rgb)
    }

    /// Get all labels as region indices (for lookup in color table)
    pub fn labels_as_indices(&self) -> Vec<i32> {
        self.labels.clone()
    }

    /// Get vertex colors as flat array for visualization
    pub fn vertex_colors(&self) -> Vec<[f32; 3]> {
        self.labels
            .iter()
            .map(|label| {
                self.color_table
                    .get(*label)
                    .map_or([0.5, 0.5, 0.5], AnnotationEntry::color_rgb) // Gray for unknown
            })
            .collect()
    }

    /// Get unique labels present in this annotation
    pub fn unique_labels(&self) -> Vec<i32> {
        let mut unique: Vec<i32> = self.labels.clone();
        unique.sort_unstable();
        unique.dedup();
        unique
    }
}

/// Read a FreeSurfer annotation file
///
/// # Arguments
///
/// * `path` - Path to the .annot file
/// * `atlas` - Atlas name (e.g., "aparc")
/// * `hemisphere` - Hemisphere of the annotation
///
/// # Format
///
/// The .annot file format (all little-endian):
/// 1. n_vertices (int32)
/// 2. For each vertex: vertex_index (int32), label (int32)
/// 3. has_colortable (int32, 0 or 1)
/// 4. If has_colortable: color table data
///
/// # Example
///
/// ```ignore
/// use rtx_neuro_anatomy::annotation::{read_annotation, Hemisphere};
///
/// let annot = read_annotation(
///     "/path/to/subject/label/lh.aparc.annot",
///     "aparc",
///     Hemisphere::Left,
/// )?;
/// println!("Loaded {} vertices", annot.n_vertices());
/// ```
pub fn read_annotation(
    path: impl AsRef<Path>,
    atlas: &str,
    hemisphere: Hemisphere,
) -> Result<Annotation> {
    let path = path.as_ref();
    let file = File::open(path).map_err(|_| AnatomyError::AnnotationNotFound {
        path: path.to_path_buf(),
    })?;
    let mut reader = BufReader::new(file);

    // Read number of vertices
    let n_vertices = reader.read_i32::<LittleEndian>()? as usize;

    // Read vertex labels
    let mut labels = vec![0i32; n_vertices];
    let mut max_vertex = 0usize;

    for _ in 0..n_vertices {
        let vertex_idx = reader.read_i32::<LittleEndian>()? as usize;
        let label = reader.read_i32::<LittleEndian>()?;

        if vertex_idx < n_vertices {
            labels[vertex_idx] = label;
            max_vertex = max_vertex.max(vertex_idx);
        }
    }

    // Check if there's a color table
    let has_colortable = reader.read_i32::<LittleEndian>()? != 0;

    let color_table = if has_colortable {
        read_colortable(&mut reader)?
    } else {
        ColorTable::default()
    };

    Ok(Annotation {
        labels,
        color_table,
        atlas: atlas.to_string(),
        hemisphere,
    })
}

/// Read the color table from an annotation file
fn read_colortable(reader: &mut BufReader<File>) -> Result<ColorTable> {
    // Read number of entries
    let num_entries = reader.read_i32::<LittleEndian>()? as usize;

    if num_entries == 0 {
        return Ok(ColorTable::default());
    }

    // Check for new format (version > 0)
    let version_or_len = reader.read_i32::<LittleEndian>()?;

    let entries = if version_or_len > 0 {
        // New format: version_or_len is the length of the original filename
        read_colortable_new(reader, num_entries, version_or_len)?
    } else {
        // Old format (not commonly used)
        read_colortable_old(reader, num_entries)?
    };

    Ok(ColorTable { entries })
}

/// Read new format color table
fn read_colortable_new(
    reader: &mut BufReader<File>,
    num_entries: usize,
    filename_len: i32,
) -> Result<HashMap<i32, AnnotationEntry>> {
    // Skip the original filename
    let mut filename_buf = vec![0u8; filename_len as usize];
    reader.read_exact(&mut filename_buf)?;

    // Read number of entries again (redundant in new format)
    let _num_entries_check = reader.read_i32::<LittleEndian>()?;

    let mut entries = HashMap::new();

    for _ in 0..num_entries {
        // Read structure number (label ID)
        let struct_id = reader.read_i32::<LittleEndian>()?;

        // Read name length and name
        let name_len = reader.read_i32::<LittleEndian>()? as usize;
        let mut name_buf = vec![0u8; name_len];
        reader.read_exact(&mut name_buf)?;

        // Remove null terminator if present
        let name = String::from_utf8_lossy(&name_buf)
            .trim_end_matches('\0')
            .to_string();

        // Read RGBA values
        let r = reader.read_i32::<LittleEndian>()? as u8;
        let g = reader.read_i32::<LittleEndian>()? as u8;
        let b = reader.read_i32::<LittleEndian>()? as u8;
        let a = reader.read_i32::<LittleEndian>()? as u8;

        // Compute the packed label value (same as what's stored per-vertex)
        let label = pack_rgba(r, g, b, a);

        entries.insert(label, AnnotationEntry { name, r, g, b, a });

        // Also insert by struct_id for direct lookup
        if struct_id != label {
            entries.insert(
                struct_id,
                AnnotationEntry {
                    name: entries[&label].name.clone(),
                    r,
                    g,
                    b,
                    a,
                },
            );
        }
    }

    Ok(entries)
}

/// Read old format color table (rarely used)
fn read_colortable_old(
    reader: &mut BufReader<File>,
    num_entries: usize,
) -> Result<HashMap<i32, AnnotationEntry>> {
    let mut entries = HashMap::new();

    // Skip filename length that was already read as version
    let filename_len = reader.read_i32::<LittleEndian>()? as usize;
    let mut filename_buf = vec![0u8; filename_len];
    reader.read_exact(&mut filename_buf)?;

    for _ in 0..num_entries {
        // Read name length and name
        let name_len = reader.read_i32::<LittleEndian>()? as usize;
        let mut name_buf = vec![0u8; name_len];
        reader.read_exact(&mut name_buf)?;

        let name = String::from_utf8_lossy(&name_buf)
            .trim_end_matches('\0')
            .to_string();

        // Read RGBA values
        let r = reader.read_i32::<LittleEndian>()? as u8;
        let g = reader.read_i32::<LittleEndian>()? as u8;
        let b = reader.read_i32::<LittleEndian>()? as u8;
        let a = reader.read_i32::<LittleEndian>()? as u8;

        let label = pack_rgba(r, g, b, a);

        entries.insert(label, AnnotationEntry { name, r, g, b, a });
    }

    Ok(entries)
}

/// Pack RGBA values into a single i32 label value
///
/// FreeSurfer packs colors as: R + G*256 + B*65536 + A*16777216
fn pack_rgba(r: u8, g: u8, b: u8, a: u8) -> i32 {
    (r as i32) + (g as i32) * 256 + (b as i32) * 65536 + (a as i32) * 16777216
}

/// Unpack i32 label value into RGBA components
pub fn unpack_rgba(label: i32) -> (u8, u8, u8, u8) {
    let r = (label & 0xFF) as u8;
    let g = ((label >> 8) & 0xFF) as u8;
    let b = ((label >> 16) & 0xFF) as u8;
    let a = ((label >> 24) & 0xFF) as u8;
    (r, g, b, a)
}

/// Get the annotation filename for an atlas
pub fn annotation_filename(hemisphere: &Hemisphere, atlas: &str) -> String {
    format!("{}.{}.annot", hemisphere.prefix(), atlas)
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_pack_unpack_rgba() {
        let r = 128u8;
        let g = 64u8;
        let b = 32u8;
        let a = 0u8;

        let packed = pack_rgba(r, g, b, a);
        let (ur, ug, ub, ua) = unpack_rgba(packed);

        assert_eq!(r, ur);
        assert_eq!(g, ug);
        assert_eq!(b, ub);
        assert_eq!(a, ua);
    }

    #[test]
    fn test_annotation_entry_colors() {
        let entry = AnnotationEntry {
            name: "test".to_string(),
            r: 255,
            g: 128,
            b: 0,
            a: 0,
        };

        let rgb = entry.color_rgb();
        assert!((rgb[0] - 1.0).abs() < 1e-6);
        assert!((rgb[1] - 0.502).abs() < 0.01);
        assert!((rgb[2] - 0.0).abs() < 1e-6);
    }

    #[test]
    fn test_annotation_filename() {
        assert_eq!(
            annotation_filename(&Hemisphere::Left, "aparc"),
            "lh.aparc.annot"
        );
        assert_eq!(
            annotation_filename(&Hemisphere::Right, "aparc.a2009s"),
            "rh.aparc.a2009s.annot"
        );
    }

    #[test]
    fn test_color_table_operations() {
        let mut entries = HashMap::new();
        entries.insert(
            1,
            AnnotationEntry {
                name: "region1".to_string(),
                r: 255,
                g: 0,
                b: 0,
                a: 0,
            },
        );
        entries.insert(
            2,
            AnnotationEntry {
                name: "region2".to_string(),
                r: 0,
                g: 255,
                b: 0,
                a: 0,
            },
        );

        let table = ColorTable { entries };

        assert_eq!(table.n_regions(), 2);
        assert!(table.get(1).is_some());
        assert!(table.get(3).is_none());

        let names = table.region_names();
        assert!(names.contains(&"region1"));
        assert!(names.contains(&"region2"));
    }
}