turnbull: Custom CSV implementation

Avoid unnecessary String allocation
13% speedup

src/csv.rs

@@ -0,0 +1,133 @@
+// hpstat: High-performance statistics implementations
+// Copyright © 2023  Lee Yingtong Li (RunasSudo)
+// 
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+// 
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Affero General Public License for more details.
+// 
+// You should have received a copy of the GNU Affero General Public License
+// along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+use std::io::BufRead;
+
+pub fn read_csv<R: BufRead>(mut reader: R) -> (Vec<String>, Vec<f64>) {
+	// This custom CSV parser is faster than the csv library because we do not waste time allocating Strings for the data which will inevitably be parsed to float anyway
+	
+	// Reuse a single buffer to avoid unnecessary allocations
+	// Since we need to make copies only for the headers - the data are directly parsed to float
+	let mut buffer = String::new();
+	
+	// Read header
+	let headers = read_row_as_strings(&mut reader, &mut buffer);
+	
+	// Read data
+	let mut data = Vec::new();
+	let mut row = Vec::new();
+	loop {
+		if read_row_as_floats(&mut reader, &mut buffer, &mut row) {
+			if row.len() != headers.len() {
+				panic!("Expected row of {} entries, got {} entries", headers.len(), row.len());
+			}
+			
+			data.append(&mut row);
+		} else {
+			// EOF
+			break;
+		}
+	}
+	
+	return (headers, data);
+}
+
+fn read_row_as_strings<R: BufRead>(reader: &mut R, buffer: &mut String) -> Vec<String> {
+	buffer.clear();
+	
+	let bytes_read = reader.read_line(buffer).expect("IO error");
+	if bytes_read == 0 {
+		panic!("Unexpected EOF");
+	}
+	
+	let mut result = Vec::new();
+	let mut entries_iter = buffer.trim().split(',');
+	loop {
+		if let Some(entry) = entries_iter.next() {
+			if entry.starts_with('"') {
+				if entry.ends_with('"') {
+					result.push(String::from(&entry[1..(entry.len() - 1)]));
+				} else {
+					let mut full_entry = String::from(&entry[1..]);
+					
+					// Read remainder of quoted entry
+					loop {
+						if let Some(entry_part) = entries_iter.next() {
+							if entry_part.ends_with('"') {
+								// End of quoted entry
+								full_entry.push_str(&entry_part[..(entry_part.len() - 1)]);
+								result.push(full_entry);
+								break;
+							} else {
+								// Middle of quoted entry
+								full_entry.push_str(entry_part);
+								full_entry.push_str(&",");
+							}
+						} else {
+							panic!("Unexpected EOL while reading quoted CSV entry");
+						}
+					}
+				}
+			} else {
+				result.push(String::from(entry));
+			}
+		} else {
+			// EOL
+			break;
+		}
+	}
+	
+	return result;
+}
+
+fn read_row_as_floats<R: BufRead>(reader: &mut R, buffer: &mut String, row: &mut Vec<f64>) -> bool {
+	buffer.clear();
+	
+	let bytes_read = reader.read_line(buffer).expect("IO error");
+	if bytes_read == 0 {
+		// EOF
+		return false;
+	}
+	
+	let mut entries_iter = buffer.trim().split(',');
+	loop {
+		if let Some(entry) = entries_iter.next() {
+			if entry.starts_with('"') {
+				if entry.ends_with('"') {
+					row.push(parse_float(&entry[1..(entry.len() - 1)]));
+				} else {
+					// Float cannot have a comma in it
+					panic!("Malformed float");
+				}
+			} else {
+				row.push(parse_float(entry));
+			}
+		} else {
+			// EOL
+			break;
+		}
+	}
+	
+	return true;
+}
+
+fn parse_float(s: &str) -> f64 {
+	let value = match s {
+		"inf" => f64::INFINITY,
+		_ => s.parse().expect("Malformed float")
+	};
+	return value;
+}

src/lib.rs

@@ -1,5 +1,6 @@
 pub mod intcox;
 pub mod turnbull;
 
+mod csv;
 mod pava;
 mod term;

src/turnbull.rs

@@ -17,17 +17,17 @@
 const Z_97_5: f64 = 1.959964;  // This is the limit of resolution for an f64
 const CHI2_1DF_95: f64 = 3.8414588;
 
-use core::mem::MaybeUninit;
-use std::io;
+use std::fs::File;
+use std::io::{self, BufReader};
 
 use clap::{Args, ValueEnum};
-use csv::{Reader, StringRecord};
 use indicatif::{ParallelProgressIterator, ProgressBar, ProgressDrawTarget, ProgressStyle};
-use nalgebra::{Const, DMatrix, DVector, Dyn, Matrix2xX};
+use nalgebra::{DMatrix, DVector, Matrix2xX};
 use prettytable::{Table, format, row};
 use rayon::prelude::*;
 use serde::{Serialize, Deserialize};
 
+use crate::csv::read_csv;
 use crate::pava::monotonic_regression_pava;
 use crate::term::UnconditionalTermLike;
 
@@ -134,45 +134,21 @@ pub fn main(args: TurnbullArgs) {
 
 pub fn read_data(path: &str) -> Matrix2xX<f64> {
 	// Read CSV into memory
-	let _headers: StringRecord;
-	let records: Vec<StringRecord>;
-	if path == "-" {
-		let mut csv_reader = Reader::from_reader(io::stdin());
-		_headers = csv_reader.headers().unwrap().clone();
-		records = csv_reader.records().map(|r| r.unwrap()).collect();
-	} else {
-		let mut csv_reader = Reader::from_path(path).unwrap();
-		_headers = csv_reader.headers().unwrap().clone();
-		records = csv_reader.records().map(|r| r.unwrap()).collect();
-	}
+	let (_headers, records) = match path {
+		"-" => read_csv(io::stdin().lock()),
+		_ => read_csv(BufReader::new(File::open(path).expect("IO error")))
+	};
 	
 	// Read data into matrices
 	
 	// Represent data_times as 2xX rather than Xx2 matrix to allow par_column_iter in code_times_as_indexes (no par_row_iter)
-	let mut data_times: Matrix2xX<MaybeUninit<f64>> = Matrix2xX::uninit(
-		Const::<2>,  // Left time, right time
-		Dyn(records.len())
-	);
-	
-	// Parse data
-	for (i, row) in records.iter().enumerate() {
-		for (j, item) in row.iter().enumerate() {
-			let value = match item {
-				"inf" => f64::INFINITY,
-				_ => item.parse().expect("Malformed float")
-			};
-			
-			data_times[(j, i)].write(value);
-		}
-	}
+	// Serendipitously, from_vec fills column-by-column
+	let data_times = Matrix2xX::from_vec(records);
 	
 	// TODO: Fail on left time > right time
 	// TODO: Fail on left time < 0
 	
-	// SAFETY: assume_init is OK because we initialised all values above
-	unsafe {
-		return data_times.assume_init();
-	}
+	return data_times;
 }
 
 struct TurnbullData {