use crate::error::Error;
use ndarray::Array2;
use ome_metadata::Ome;
use serde::{Deserialize, Serialize};
use std::fmt::Debug;
use std::path::{Path, PathBuf};

use crate::readers::{ArrayT, DynReader, Frame, PixelType, Reader, Shape};
use itertools::Itertools;
use j4rs::{Instance, InvocationArg, JavaOpt, Jvm, JvmBuilder};
use std::cell::OnceCell;
use std::collections::HashSet;
use std::hash::{Hash, Hasher};
use std::ops::Deref;
use std::rc::Rc;
use std::sync::Mutex;
use thread_local::ThreadLocal;

include!(concat!(env!("OUT_DIR"), "/constants.rs"));

thread_local! {
    static JVM: OnceCell<Rc<Jvm>> = const { OnceCell::new() }
}

static DOWNLOAD_LOCK: Mutex<()> = Mutex::new(());
static JVM_BUILT: Mutex<bool> = Mutex::new(false);

/// Ensure 1 jvm per thread
fn jvm() -> Rc<Jvm> {
    JVM.with(|cell| {
        cell.get_or_init(move || {
            #[cfg(feature = "python")]
            let path = crate::py::ndbioimage_file();

            #[cfg(not(feature = "python"))]
            let path = std::env::current_exe()
                .unwrap()
                .parent()
                .unwrap()
                .to_path_buf();

            let class_path = if path.join("jassets").exists() {
                path.as_path()
            } else {
                path.parent().unwrap()
            };

            // download jars if needed, but make sure only one thread will do this
            {
                let _guard = DOWNLOAD_LOCK.lock().unwrap();
                let jassets = class_path.join("jassets");
                if !jassets.exists() {
                    std::fs::create_dir_all(&jassets).unwrap();
                }

                if !jassets.join(format!("j4rs-{}-jar-with-dependencies.jar", J4RS_VERSION)).exists() {
                    println!("downloading j4rs-{}-jar-with-dependencies.jar into {}", J4RS_VERSION, jassets.display());
                    let download = downloader::Download::new(&format!(
                        "https://github.com/astonbitecode/j4rs/raw/v{}/rust/jassets/j4rs-{}-jar-with-dependencies.jar",
                        J4RS_VERSION, J4RS_VERSION
                    ));
                    let mut downloader = downloader::Downloader::builder()
                        .download_folder(&jassets)
                        .build().unwrap();
                    downloader
                        .download(&[download]).unwrap()
                        .into_iter()
                        .collect::<Result<Vec<_>, _>>().unwrap();
                }

                if !jassets.join(format!("bioformats_package-{}.jar", BIOFORMATS_VERSION)).exists() {
                    println!("downloading bioformats_package-{}.jar into {}", BIOFORMATS_VERSION, jassets.display());
                    let download = downloader::Download::new(&format!(
                        "https://artifacts.openmicroscopy.org/artifactory/ome.releases/ome/bioformats_package/{}/bioformats_package-{}.jar",
                        BIOFORMATS_VERSION, BIOFORMATS_VERSION
                    ));
                    let mut downloader = downloader::Downloader::builder()
                        .download_folder(&jassets)
                        .build().unwrap();
                    downloader
                        .download(&[download]).unwrap()
                        .into_iter()
                        .collect::<Result<Vec<_>, _>>().unwrap();
                }

                #[cfg(feature = "gpl-formats")]
                if !jassets.join(format!("formats-gpl-{}.jar", BIOFORMATS_VERSION)).exists() {
                    println!("downloading formats-gpl-{}.jar into {}", BIOFORMATS_VERSION, jassets.display());
                    let download = downloader::Download::new(&format!(
                        "https://artifacts.openmicroscopy.org/artifactory/ome.releases/ome/formats-gpl/{}/formats-gpl-{}.jar",
                        BIOFORMATS_VERSION, BIOFORMATS_VERSION
                    ));
                    let mut downloader = downloader::Downloader::builder()
                        .download_folder(&jassets)
                        .build().unwrap();
                    downloader
                        .download(&[download]).unwrap()
                        .into_iter()
                        .collect::<Result<Vec<_>, _>>().unwrap();
                }
            }
            {
                let mut jvm_built = JVM_BUILT.lock().unwrap();
                Rc::new(if *jvm_built {
                    Jvm::attach_thread().expect("Failed to attach to JVM")
                } else {
                    *jvm_built = true;
                    let j = JvmBuilder::new()
                        .skip_setting_native_lib()
                        .with_base_path(class_path.to_str().unwrap())
                        .java_opt(JavaOpt::new("-XX:+IgnoreUnrecognizedVMOptions"))
                        .java_opt(JavaOpt::new("--enable-native-access=ALL-UNNAMED"))
                        .java_opt(JavaOpt::new("--sun-misc-unsafe-memory-access=allow"))
                        .build()
                        .expect("Failed to build JVM");
                    if let Ok(e) = InvocationArg::try_from("ERROR") {
                        let _ = j.invoke_static(
                            "loci.common.DebugTools",
                            "setRootLevel",
                            &[e],
                        );
                    }
                    j
                })
            }
        })
            .clone()
    })
}

macro_rules! method_return {
    ($R:ty$(|c)?) => { Result<$R, Error> };
    () => { Result<(), Error> };
}

macro_rules! method_arg {
    ($n:tt: $t:ty|p) => {
        InvocationArg::try_from($n)?.into_primitive()?
    };
    ($n:tt: $t:ty) => {
        InvocationArg::try_from($n)?
    };
}

macro_rules! method {
    ($name:ident, $method:expr $(,[$($n:tt: $t:ty$(|$p:tt)?),*])? $(=> $tt:ty$(|$c:tt)?)?) => {
        #[allow(dead_code)]
        pub(crate) fn $name(&self, $($($n: $t),*)?) -> method_return!($($tt)?) {
            let args: Vec<InvocationArg> = vec![$($( method_arg!($n:$t$(|$p)?) ),*)?];
            let _result = jvm().invoke(&self.0, $method, &args)?;

            macro_rules! method_result {
                ($R:ty|c) => {
                    Ok(jvm().to_rust(_result)?)
                };
                ($R:ty|d) => {
                    Ok(jvm().to_rust_deserialized(_result)?)
                };
                ($R:ty) => {
                    Ok(_result)
                };
                () => {
                    Ok(())
                };
            }

            method_result!($($tt$(|$c)?)?)
        }
    };
}

fn transmute_vec<T, U>(vec: Vec<T>) -> Vec<U> {
    unsafe {
        // Ensure the original vector is not dropped.
        let mut v_clone = std::mem::ManuallyDrop::new(vec);
        Vec::from_raw_parts(
            v_clone.as_mut_ptr() as *mut U,
            v_clone.len(),
            v_clone.capacity(),
        )
    }
}

/// Wrapper around bioformats java class loci.common.DebugTools
pub struct DebugTools;

impl DebugTools {
    /// set debug root level: ERROR, DEBUG, TRACE, INFO, OFF
    pub fn set_root_level(level: &str) -> Result<(), Error> {
        jvm().invoke_static(
            "loci.common.DebugTools",
            "setRootLevel",
            &[InvocationArg::try_from(level)?],
        )?;
        Ok(())
    }
}

/// Wrapper around bioformats java class loci.formats.ChannelSeparator
pub(crate) struct ChannelSeparator(Instance);

impl ChannelSeparator {
    pub(crate) fn new(image_reader: &ImageReader) -> Result<Self, Error> {
        let jvm = jvm();
        let channel_separator = jvm.create_instance(
            "loci.formats.ChannelSeparator",
            &[InvocationArg::from(jvm.clone_instance(&image_reader.0)?)],
        )?;
        Ok(ChannelSeparator(channel_separator))
    }

    pub(crate) fn open_bytes(&self, index: i32) -> Result<Vec<u8>, Error> {
        Ok(transmute_vec(self.open_bi8(index)?))
    }

    method!(open_bi8, "openBytes", [index: i32|p] => Vec<i8>|c);
    method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c);
}

/// Wrapper around bioformats java class loci.formats.ImageReader
pub struct ImageReader(Instance);

impl Drop for ImageReader {
    fn drop(&mut self) {
        self.close().unwrap()
    }
}

impl ImageReader {
    pub(crate) fn new() -> Result<Self, Error> {
        let reader = jvm().create_instance("loci.formats.ImageReader", InvocationArg::empty())?;
        Ok(ImageReader(reader))
    }

    pub(crate) fn open_bytes(&self, index: i32) -> Result<Vec<u8>, Error> {
        Ok(transmute_vec(self.open_bi8(index)?))
    }

    pub(crate) fn ome_xml(&self) -> Result<String, Error> {
        let mds = self.get_metadata_store()?;
        Ok(jvm()
            .chain(&mds)?
            .cast("loci.formats.ome.OMEPyramidStore")?
            .invoke("dumpXML", InvocationArg::empty())?
            .to_rust()?)
    }

    method!(close, "close");
    method!(is_indexed, "isIndexed" => bool|c);
    method!(is_interleaved, "isInterleaved" => bool|c);
    method!(is_little_endian, "isLittleEndian" => bool|c);
    method!(is_rgb, "isRGB" => bool|c);
    method!(get_8bit_lookup_table, "get8BitLookupTable" => Instance);
    method!(get_16bit_lookup_table, "get16BitLookupTable" => Instance);
    method!(get_dimension_order, "getDimensionOrder" => String|c);
    method!(set_id, "setId", [id: &str]);
    method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c);
    method!(set_metadata_store, "setMetadataStore", [ome_data: Instance]);
    method!(get_metadata_store, "getMetadataStore" => Instance);
    method!(get_pixel_type, "getPixelType" => i32|c);
    method!(get_rgb_channel_count, "getRGBChannelCount" => i32|c);
    method!(get_series, "getSeries" => i32|c);
    method!(set_series, "setSeries", [series: i32|p]);
    method!(get_series_count, "getSeriesCount" => i32|c);
    method!(get_size_x, "getSizeX" => i32|c);
    method!(get_size_y, "getSizeY" => i32|c);
    method!(get_size_c, "getSizeC" => i32|c);
    method!(get_size_t, "getSizeT" => i32|c);
    method!(get_size_z, "getSizeZ" => i32|c);
    method!(open_bi8, "openBytes", [index: i32|p] => Vec<i8>|c);
}

/// Wrapper around bioformats java class loci.formats.MetadataTools
pub(crate) struct MetadataTools(Instance);

impl MetadataTools {
    pub(crate) fn new() -> Result<Self, Error> {
        let meta_data_tools =
            jvm().create_instance("loci.formats.MetadataTools", InvocationArg::empty())?;
        Ok(MetadataTools(meta_data_tools))
    }

    method!(create_ome_xml_metadata, "createOMEXMLMetadata" => Instance);
}

/// Reader interface to file. Use get_frame to get data.
#[derive(Serialize, Deserialize)]
pub struct BioFormatsJavaReader {
    #[serde(skip)]
    reader: ThreadLocal<ImageReader>,
    /// path to file
    path: PathBuf,
    /// which (if more than 1) of the series in the file to open
    series: usize,
    shape: Shape,
    pixel_type: PixelType,
    little_endian: bool,
}

impl From<BioFormatsJavaReader> for DynReader {
    fn from(value: BioFormatsJavaReader) -> Self {
        DynReader::BioFormatsJava(value)
    }
}

impl Hash for BioFormatsJavaReader {
    fn hash<H: Hasher>(&self, state: &mut H) {
        self.path.hash(state);
        self.series.hash(state);
    }
}

impl PartialEq for BioFormatsJavaReader {
    fn eq(&self, other: &Self) -> bool {
        self.path == other.path
            && self.series == other.series
            && self.shape == other.shape
            && self.pixel_type == other.pixel_type
            && self.little_endian == other.little_endian
    }
}

impl Eq for BioFormatsJavaReader {}

impl Deref for BioFormatsJavaReader {
    type Target = ImageReader;

    fn deref(&self) -> &Self::Target {
        self.get_reader().unwrap()
    }
}

impl Clone for BioFormatsJavaReader {
    fn clone(&self) -> Self {
        // BioFormatsReader::new(&self.path, self.series, 0).unwrap()
        Self {
            reader: ThreadLocal::default(),
            path: self.path.clone(),
            series: self.series,
            shape: self.shape.clone(),
            pixel_type: self.pixel_type,
            little_endian: self.little_endian,
        }
    }
}

impl Debug for BioFormatsJavaReader {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
        f.debug_struct("BioFormatsJavaReader")
            .field("path", &self.path)
            .field("series", &self.series)
            .field("shape", &self.shape)
            .field("pixel_type", &self.pixel_type)
            .field("little_endian", &self.little_endian)
            .finish()
    }
}

impl BioFormatsJavaReader {
    fn get_reader(&self) -> Result<&ImageReader, Error> {
        self.reader.get_or_try(|| {
            let reader = ImageReader::new()?;
            let meta_data_tools = MetadataTools::new()?;
            let ome_meta = meta_data_tools.create_ome_xml_metadata()?;
            reader.set_metadata_store(ome_meta)?;
            reader.set_id(self.path.to_str().ok_or(Error::InvalidFileName)?)?;
            reader.set_series(self.series as i32)?;
            Ok(reader)
        })
    }

    // pub fn set_reader(&self) -> Result<(), Error> {
    //     self.get_reader().map(|_| ())
    // }

    /// Get ome metadata as ome structure
    pub fn get_ome(&self) -> Result<Ome, Error> {
        let mut ome = Ome::from_xml(self.ome_xml()?)?;
        if ome.image.len() > 1 {
            ome.image = vec![ome.image[self.series].clone()];
        }
        Ok(ome)
    }

    /// Get ome metadata as xml string
    pub fn get_ome_xml(&self) -> Result<String, Error> {
        self.ome_xml()
    }

    fn deinterleave(&self, bytes: Vec<u8>, channel: usize) -> Result<Vec<u8>, Error> {
        let chunk_size = match self.pixel_type {
            PixelType::Bool => 1,
            PixelType::I8 => 1,
            PixelType::U8 => 1,
            PixelType::I16 => 2,
            PixelType::U16 => 2,
            PixelType::I32 => 4,
            PixelType::U32 => 4,
            PixelType::F32 => 4,
            PixelType::F64 => 8,
            PixelType::I64 => 8,
            PixelType::U64 => 8,
            PixelType::I128 => 16,
            PixelType::U128 => 16,
            PixelType::F128 => 8,
        };
        Ok(bytes
            .chunks(chunk_size)
            .skip(channel)
            .step_by(self.shape.c)
            .flat_map(|a| a.to_vec())
            .collect())
    }

    fn bytes_to_frame(&self, bytes: Vec<u8>) -> Result<Frame, Error> {
        macro_rules! get_frame {
            (bool, <$n:expr) => {
                Ok(ArrayT::from(Array2::from_shape_vec(
                    (self.shape.y, self.shape.x),
                    bytes
                        .iter()
                        .map(|x| [x & 128, x & 64, x & 32, x & 16, x & 8, x & 4, x & 2, x & 1])
                        .flatten()
                        .collect(),
                )?))
            };
            (bool, >$n:expr) => {
                Ok(ArrayT::from(Array2::from_shape_vec(
                    (self.shape.y, self.shape.x),
                    bytes
                        .iter()
                        .map(|x| [x & 1, x & 2, x & 4, x & 8, x & 16, x & 32, x & 64, x & 128])
                        .flatten()
                        .collect(),
                )?))
            };
            ($t:tt, <$n:expr) => {
                Ok(ArrayT::from(Array2::from_shape_vec(
                    (self.shape.y, self.shape.x),
                    bytes
                        .chunks($n)
                        .map(|x| $t::from_le_bytes(x.try_into().unwrap()))
                        .collect(),
                )?))
            };
            ($t:tt, >$n:expr) => {
                Ok(ArrayT::from(Array2::from_shape_vec(
                    (self.shape.y, self.shape.x),
                    bytes
                        .chunks($n)
                        .map(|x| $t::from_be_bytes(x.try_into().unwrap()))
                        .collect(),
                )?))
            };
        }

        match (&self.pixel_type, self.little_endian) {
            (PixelType::Bool, true) => get_frame!(bool, <1),
            (PixelType::I8, true) => get_frame!(i8, <1),
            (PixelType::U8, true) => get_frame!(u8, <1),
            (PixelType::I16, true) => get_frame!(i16, <2),
            (PixelType::U16, true) => get_frame!(u16, <2),
            (PixelType::I32, true) => get_frame!(i32, <4),
            (PixelType::U32, true) => get_frame!(u32, <4),
            (PixelType::F32, true) => get_frame!(f32, <4),
            (PixelType::F64, true) => get_frame!(f64, <8),
            (PixelType::I64, true) => get_frame!(i64, <8),
            (PixelType::U64, true) => get_frame!(u64, <8),
            (PixelType::I128, true) => get_frame!(i128, <16),
            (PixelType::U128, true) => get_frame!(u128, <16),
            (PixelType::F128, true) => get_frame!(f64, <8),
            (PixelType::Bool, false) => get_frame!(bool, >1),
            (PixelType::I8, false) => get_frame!(i8, >1),
            (PixelType::U8, false) => get_frame!(u8, >1),
            (PixelType::I16, false) => get_frame!(i16, >2),
            (PixelType::U16, false) => get_frame!(u16, >2),
            (PixelType::I32, false) => get_frame!(i32, >4),
            (PixelType::U32, false) => get_frame!(u32, >4),
            (PixelType::F32, false) => get_frame!(f32, >4),
            (PixelType::F64, false) => get_frame!(f64, >8),
            (PixelType::I64, false) => get_frame!(i64, >8),
            (PixelType::U64, false) => get_frame!(u64, >8),
            (PixelType::I128, false) => get_frame!(i128, >16),
            (PixelType::U128, false) => get_frame!(u128, >16),
            (PixelType::F128, false) => get_frame!(f64, >8),
        }
    }
}

impl Drop for BioFormatsJavaReader {
    fn drop(&mut self) {
        if let Ok(reader) = self.get_reader() {
            reader.close().unwrap();
        }
    }
}

fn find_tiff(path: &Path) -> Result<Option<PathBuf>, Error> {
    if let Some(ext) = path.extension()
        && path.is_file()
        && (["tif", "tiff"].contains(&ext.to_string_lossy().to_lowercase().as_str()))
    {
        return Ok(Some(path.to_path_buf()));
    } else if path.is_dir() {
        for file in path.read_dir()?.flatten().sorted_by_key(|i| i.file_name()) {
            if let Ok(Some(file)) = find_tiff(file.path().as_path()) {
                return Ok(Some(file));
            }
        }
    }
    Ok(None)
}

impl Reader for BioFormatsJavaReader {
    /// Create a new reader for the image file at a path, and open series #.
    fn new<P>(path: P, series: usize, _position: usize) -> Result<Self, Error>
    where
        P: AsRef<Path>,
    {
        let mut path = path.as_ref().to_path_buf();
        if path.is_dir() {
            let orig = path.clone();
            path = find_tiff(&path)?.ok_or_else(|| {
                Error::FileDoesNotExist(orig.join("**").join("*.tif").display().to_string())
            })?;
        }
        let mut new = Self {
            reader: ThreadLocal::default(),
            path,
            series,
            shape: Shape::default(),
            pixel_type: PixelType::I8,
            little_endian: false,
        };
        // new.set_reader()?;
        new.shape.x = new.get_size_x()? as usize;
        new.shape.y = new.get_size_y()? as usize;
        new.shape.c = new.get_size_c()? as usize;
        new.shape.z = new.get_size_z()? as usize;
        new.shape.t = new.get_size_t()? as usize;
        new.pixel_type = PixelType::try_from(new.get_pixel_type()?)?;
        new.little_endian = new.is_little_endian()?;
        Ok(new)
    }

    fn metadata(&self) -> Result<Ome, Error> {
        self.get_ome()
    }

    /// Retrieve fame at channel c, slize z and time t.
    fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame, Error> {
        let bytes = if self.is_rgb()? && self.is_interleaved()? {
            let index = self.get_index(z as i32, 0, t as i32)?;
            self.deinterleave(self.open_bytes(index)?, c)?
        } else if self.get_rgb_channel_count()? > 1 {
            let channel_separator = ChannelSeparator::new(self)?;
            let index = channel_separator.get_index(z as i32, c as i32, t as i32)?;
            channel_separator.open_bytes(index)?
        } else {
            let index = self.get_index(z as i32, c as i32, t as i32)?;
            self.open_bytes(index)?
        };
        self.bytes_to_frame(bytes)
    }

    fn path(&self) -> &Path {
        &self.path
    }

    fn series(&self) -> usize {
        self.series
    }

    fn position(&self) -> usize {
        0
    }

    fn shape(&self) -> &Shape {
        &self.shape
    }

    fn pixel_type(&self) -> &PixelType {
        &self.pixel_type
    }

    fn get_available_positions<P>(_path: P, _series: usize) -> Result<HashSet<usize>, Error>
    where
        P: AsRef<Path>,
    {
        Ok(HashSet::from([0]))
    }

    fn get_available_series<P>(path: P) -> Result<HashSet<usize>, Error>
    where
        P: AsRef<Path>,
    {
        let mut path = path.as_ref().to_path_buf();
        if path.is_dir() {
            let orig = path.clone();
            path = find_tiff(&path)?.ok_or_else(|| {
                Error::FileDoesNotExist(orig.join("**").join("*.tif").display().to_string())
            })?;
        }
        let new = BioFormatsJavaReader {
            reader: ThreadLocal::default(),
            path,
            series: 0,
            shape: Shape::default(),
            pixel_type: PixelType::I8,
            little_endian: false,
        };
        Ok(HashSet::from_iter(0..(new.get_series_count()? as usize)))
    }
}

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

    fn open(file: &str) -> Result<BioFormatsJavaReader, Error> {
        let path = std::env::current_dir()?
            .join("tests")
            .join("files")
            .join(file);
        BioFormatsJavaReader::new(&path, 0, 0)
    }

    macro_rules! test_metadata {
        ($($name:ident: $file:expr $(,)?)*) => {
            $(
                #[test]
                fn $name() -> Result<(), Error> {
                    let bf = open($file)?;
                    println!("{}", bf.view().squeeze()?.summary()?);
                    Ok(())
                }
            )*
        };
    }

    test_metadata! {
        metadata_a: "czi/1xp53-01-AP1.czi",
        metadata_b: "czi/beads_2023_05_04__19_00_22.czi",
        metadata_c: "czi/Experiment-2029.czi",
        metadata_d: "czi/MK022_cE9_1-01-Airyscan Processing-01-Scene-2-P1.czi",
        metadata_e: "czi/YTL1849A131_2023_05_04__13_36_36.czi",
        metadata_f: "czi/EU_UV_t=1-01.czi",
        metadata_g: "tiffseq/4-Pos_001_002/img_000000000_Cy3-Cy3_filter_000.tif",
        metadata_h: "tiffseq/20-Pos_005_005/img_000000000_Cy3-Cy3_filter_000.tif",
        metadata_i: "tiffseq/YTL1841B2-2-1_1hr_DMSO_galinduction_1",
    }

    #[test]
    fn ome_xml() -> Result<(), Error> {
        let file = "czi/Experiment-2029.czi";
        let path = std::env::current_dir()?
            .join("tests")
            .join("files")
            .join(file);
        let reader = BioFormatsJavaReader::new(&path, 0, 0)?;
        let xml = reader.get_ome_xml()?;
        println!("{}", xml);
        Ok(())
    }
}