msn_kit/io/mzml_parser/
binary_conversion.rs

1// (c) Copyright 2021 Trent Hauck
2// All Rights Reserved
3
4use flate2::read::ZlibDecoder;
5use std::io::prelude::*;
6
7use crate::io::mzml_parser::types::{Binary, CompressionType, DataType};
8
9use byteorder::{LittleEndian, ReadBytesExt};
10use std::io::Cursor;
11
12/// Convert the binary content into a float of the appropriate type.
13pub fn decode_binary_array(b: &Binary, ct: &CompressionType, dt: &DataType) -> Vec<f64> {
14    let decoded = base64::decode(&b.content).expect("Unable to decode binary.");
15
16    match (ct, dt) {
17        (CompressionType::NoCompression, DataType::Float32Bit) => {
18            binary_string_to_array_f32(decoded)
19        }
20        (CompressionType::NoCompression, DataType::Float64Bit) => {
21            binary_string_to_array_f64(decoded)
22        }
23        (CompressionType::ZlibCompression, DataType::Float64Bit) => {
24            let mut decoded_bytes = Vec::<u8>::new();
25
26            let rdr = Cursor::new(decoded);
27
28            let mut d = ZlibDecoder::new(rdr);
29            d.read_to_end(&mut decoded_bytes).unwrap();
30
31            binary_string_to_array_f64(decoded_bytes)
32        }
33        (CompressionType::ZlibCompression, DataType::Float32Bit) => {
34            let mut decoded_bytes = Vec::<u8>::new();
35
36            let rdr = Cursor::new(decoded);
37
38            let mut d = ZlibDecoder::new(rdr);
39            d.read_to_end(&mut decoded_bytes).unwrap();
40
41            binary_string_to_array_f32(decoded_bytes)
42        }
43    }
44}
45
46pub fn binary_string_to_array_f32(decoded: Vec<u8>) -> Vec<f64> {
47    let mut rdr = Cursor::new(decoded);
48
49    let mut peaks = Vec::<f64>::new();
50    while let Ok(fl) = rdr.read_f32::<LittleEndian>() {
51        peaks.push(f64::from(fl));
52    }
53
54    peaks
55}
56
57pub fn binary_string_to_array_f64(decoded: Vec<u8>) -> Vec<f64> {
58    let mut rdr = Cursor::new(decoded);
59
60    let mut peaks = Vec::<f64>::new();
61    while let Ok(fl) = rdr.read_f64::<LittleEndian>() {
62        peaks.push(fl);
63    }
64
65    peaks
66}
67
68#[cfg(test)]
69mod tests {
70    use super::*;
71
72    use crate::io::mzml_parser::types::Binary;
73    use crate::io::mzml_parser::types::DataType;
74
75    #[test]
76    fn parse_mzml_test() {
77        struct TestData {
78            binary: Binary,
79            compression_type: CompressionType,
80            data_type: DataType,
81            expected_array: Vec<f64>,
82        }
83
84        impl TestData {
85            pub fn new(
86                binary: Binary,
87                compression_type: CompressionType,
88                data_type: DataType,
89                expected_array: Vec<f64>,
90            ) -> Self {
91                Self {
92                    binary,
93                    compression_type,
94                    data_type,
95                    expected_array,
96                }
97            }
98        }
99
100        let tests = vec![
101            TestData::new(Binary::new(String::from("AAAAAAAALkAAAAAAAAAsQAAAAAAAACpAAAAAAAAAKEAAAAAAAAAmQAAAAAAAACRAAAAAAAAAIkAAAAAAAAAgQAAAAAAAABxAAAAAAAAAGEAAAAAAAAAUQAAAAAAAABBAAAAAAAAACEAAAAAAAAAAQAAAAAAAAPA/")), CompressionType::NoCompression, DataType::Float64Bit, vec![15.0, 14.0, 13.0, 12.0, 11.0, 10.0, 9.0, 8.0, 7.0, 6.0, 5.0, 4.0, 3.0, 2.0, 1.0]),
102            TestData::new(Binary::new(String::from("eJxjYEABDhBKAEpLQGkFKK0CpTWgtA6UNoDSRg4AZlQDYw==")), CompressionType::ZlibCompression, DataType::Float64Bit, vec![0.0, 2.0, 4.0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0, 18.0])
103        ];
104
105        for test in tests.iter() {
106            let array = decode_binary_array(&test.binary, &test.compression_type, &test.data_type);
107            assert_eq!(array, test.expected_array);
108        }
109    }
110}
msn_kit/io/mzml_parser/binary_conversion.rs

msn_kit/io/mzml_parser/
binary_conversion.rs
