WHAM/src/io.rs

use super::histogram::Dataset;
use super::histogram::Histogram;
use super::Config;
use std::fs::File;
use std::io::prelude::*;
use std::io::{BufReader,BufWriter};
use k_B;
use std::process;
use std::option::Option;
use std::path::Path;
use std::error::Error;
use std::result::Result;

// Returns the path to path2 relative to path1
// path1: "path/to/file.dat"
// path2: "another_file.dat"
// => result = path/to/another_file.dat
fn get_relative_path(path1: &str, path2: &str) -> String {
    let path1 = Path::new(path1);
    path1.parent().unwrap().join(path2).to_str().unwrap().to_string()
}

pub fn vprintln(s: String, verbose: bool) {
    if verbose {
        println!("{}", s);
    }
}

// Read input data into a histogram set by iterating over input files
// given in the metadata file
pub fn read_data(cfg: &Config) -> Option<Dataset> {
	let mut bias_pos: Vec<f64> = Vec::new();
	let mut bias_fc: Vec<f64> = Vec::new();
    let mut histograms: Vec<Histogram> = Vec::new();

	let kT = cfg.temperature * k_B;
    let bin_width: Vec<f64> = (0..cfg.dimens).map(|idx| {
            (cfg.hist_max[idx] - cfg.hist_min[idx])/(cfg.num_bins[idx] as f64)
        }).collect();
    let num_bins = cfg.num_bins.iter().fold(1, |state, &bins| state*bins);
    let dimens_length = cfg.num_bins.clone();

    let f = File::open(&cfg.metadata_file).unwrap_or_else(|x| {
        eprintln!("Failed to read metadata from {}. {}", &cfg.metadata_file, x);
        process::exit(1)
    });
    let buf = BufReader::new(&f);

    // read each metadata file line and parse it
    for l in buf.lines() {
    	let line = l.unwrap();

        // skip comments and empty lines
        if line.starts_with("#") || line.len() == 0 {
    		continue;
    	}

    	let mut split = line.split_whitespace();

        // parse histogram data
        let path = get_relative_path(&cfg.metadata_file, split.next()?);
        match read_window_file(&path, cfg) {
            Some(h) => {
                histograms.push(h);
                vprintln(format!("{}, {} data points added.", &path, histograms.last().unwrap().num_points), cfg.verbose);
            },
            None => {
                eprintln!("No data points inside histogram boundaries: {}", &path);
                process::exit(1)
            }
        }

        // parse bias force constants and positions
        for _ in 0..cfg.dimens {
            match split.next()?.parse() {
                Ok(x) => bias_pos.push(x),
                _ => {
                    eprintln!("Failed to read bias coordinate.");
                    process::exit(1);
                }
            }
        }
        for _ in 0..cfg.dimens {
            match split.next()?.parse() {
                Ok(x) => bias_fc.push(x),
                _ => {
                    eprintln!("Failed to read bias force constant.");
                    process::exit(1);
                }
            }

        }
    }
    
    if histograms.len() > 0 {
        Some(Dataset::new(num_bins, dimens_length, bin_width, cfg.hist_min.clone(), cfg.hist_max.clone(), bias_pos, bias_fc, kT, histograms, cfg.cyclic))
    } else {
        None
    }
}

// transforms a multidimensional index into a one dimensional index
// indeces: multidimensional indeces
// lengths: length of the matrix in each dimension
// returns an index if the matrix is flattened to a one dimensional vector
// example for 3 dimensions N,M,O: idx = i_O + l_O*l_M*i_M + l_O*l_M*l_N*i_N
fn flat_index(indeces: &Vec<usize>, lengths: &Vec<usize>) -> usize {
    let mut idx = 0;
    for i in 0..indeces.len() {
        idx += indeces[i]*lengths[0..i].iter()
            .fold(1, |state, &l| { state * l });
    }
    idx
}

// returns true if the values are inside the histogram boundaries defined by cfg
fn is_in_hist_boundaries(values: &Vec<f64>, cfg: &Config) -> bool {
    for dimen in 0..cfg.dimens {
        if values[dimen] < cfg.hist_min[dimen] || values[dimen] > cfg.hist_max[dimen] {
            return false
        }
    }
    true
}

// parse a timeseries file into a histogram
fn read_window_file(window_file: &str, cfg: &Config) -> Option<Histogram> {
	let f = File::open(window_file).unwrap_or_else(|x| {
        eprintln!("Failed to read sample data from {}. {}", window_file, x);
        process::exit(1)
    });
    let mut buf = BufReader::new(&f);

    // total number of bins is the product of all dimensions length
    let total_bins = cfg.num_bins.iter().fold(1, |s, &x| { s*x });
    let mut hist = vec![0.0; total_bins];

    // bin width for each dimension: (max-min)/bins
    let bin_width: Vec<f64> = (0..cfg.dimens).map(|idx| {
            (cfg.hist_max[idx] - cfg.hist_min[idx])/(cfg.num_bins[idx] as f64)
        }).collect();

    // read and parse each timeseries line
    let mut line = String::new();
    while buf.read_line(&mut line).unwrap() > 0 {
        // skip comments and empty lines
        if line.starts_with("#") || line.starts_with("@") || line.len() == 0 {
            line.clear();
            continue;
        }

        {
            let mut split = line.split_whitespace();

            split.next(); // skip time/step column
            let values: Vec<f64> = (0..cfg.dimens).collect::<Vec<usize>>().iter().map(|_| {
                split.next().unwrap().parse::<f64>().unwrap()
            }).collect();

            if is_in_hist_boundaries(&values, cfg) {
                let bin_indeces = (0..cfg.dimens).map(|dimen: usize| {
                    let val = values[dimen];
                    ((val - cfg.hist_min[dimen]) / bin_width[dimen]) as usize
                }).collect();
                let index = flat_index(&bin_indeces, &cfg.num_bins);
                hist[index] += 1.0;
            }
        }
        line.clear();
    }

    let num_points: f64 = hist.iter().sum();
    if num_points == 0.0 {
        return None
    }
    Some(Histogram::new(num_points as u32, hist))
}

// TODO multidimensional output
pub fn write_results(out_file: &str, ds: &Dataset, free: &Vec<f64>, prob: &Vec<f64>) -> Result<(), Box<Error>> {
    let output = File::create(out_file)?;
    let mut buf = BufWriter::new(output);
    writeln!(buf, "#{}\t{}\t{}", "x", "Free Energy", "Probability"); // TODO better format (coord1, coord2..)
    for bin in 0..free.len() {
        let coords = ds.get_coords_for_bin(bin);
        let coords_str: String = coords.iter().map(|c| {format!("{:8.6}", c)})
            .collect::<Vec<String>>().join("\t");
        writeln!(buf, "{}\t{:8.6}\t{:8.6}", coords_str, free[bin], prob[bin])?;
    }
    Ok(())
}

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

    fn cfg() -> Config {
        Config {
            metadata_file: "tests/data/metadata.dat".to_string(),
            hist_min: vec![0.0],
            hist_max: vec![3.0],
            num_bins: vec![30],
            dimens: 1,
            verbose: false,
            tolerance: 0.0,
            max_iterations: 0,
            temperature: 300.0,
            cyclic: false,
            output: "qwert".to_string(),
        }
    }

    #[test]
    #[ignore] // TODO
    fn read_window_file() {
        let f = "tests/data/window_0.0.dat";
        let cfg = cfg();
        let h = super::read_window_file(&f, &cfg).unwrap();
        println!("{:?}", h);
        // assert_eq!(1, h.first);
        // assert_eq!(6, h.last);
        assert_eq!(11, h.num_points);
        assert_eq!(2.0, h.bins[1]);
        assert_eq!(2.0, h.bins[2]);
        assert_eq!(1.0, h.bins[6]);
    }


    #[test]
    #[ignore] // TODO
    fn read_data() {
        let cfg = cfg();
        let ds = super::read_data(&cfg);
        assert!(ds.is_some());
        let ds = ds.unwrap();
        println!("{:?}", ds);
        assert_eq!(2, ds.num_windows);
        assert_eq!(cfg.num_bins[0], ds.dimens_lengths[0]);
        // fields are private  
        // assert_eq!(cfg.hist_min[0], ds.hist_min[0]);
        // assert_eq!(cfg.hist_max[0], ds.hist_max[0]);
        // let expected_bin_width = (cfg.hist_max[0] - cfg.hist_min[0])/cfg.num_bins[0] as f64;
        // assert_eq!(expected_bin_width, ds.bin_width);
        // assert_eq!(vec![0.0, 1.0], ds.bias_pos);
        // assert_eq!(vec![100.0, 200.0], ds.bias_fc);
        assert_eq!(cfg.temperature * k_B, ds.kT);
        assert_eq!(2, ds.histograms.len())
    }

    #[test]
    fn get_relative_path() {
        let path1 = "path/to/some_file.dat";
        let path2 = "another_file.dat";
        let path3 = "subfolder/another_file.dat";
        let relative2 = super::get_relative_path(&path1, &path2);
        assert_eq!("path/to/another_file.dat" ,relative2);
        let relative3 = super::get_relative_path(&path1, &path3);
        assert_eq!("path/to/subfolder/another_file.dat" ,relative3);
    }
}