mscore/timstof/quadrupole.rs
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use std::collections::{HashMap, HashSet};
use std::f64;
use std::f64::consts::E;
use itertools::izip;
use crate::data::spectrum::MzSpectrum;
use crate::simulation::annotation::{MzSpectrumAnnotated, TimsFrameAnnotated};
use crate::timstof::frame::TimsFrame;
/// Sigmoid step function for quadrupole selection simulation
///
/// Arguments:
///
/// * `x` - mz values
/// * `up_start` - start of the step
/// * `up_end` - end of the step
/// * `k` - steepness of the step
///
/// Returns:
///
/// * `Vec<f64>` - transmission probability for each mz value
///
/// # Examples
///
/// ```
/// use mscore::timstof::quadrupole::smooth_step;
///
/// let mz = vec![100.0, 200.0, 300.0];
/// let transmission = smooth_step(&mz, 150.0, 250.0, 0.5).iter().map(
/// |&x| (x * 100.0).round() / 100.0).collect::<Vec<f64>>();
/// assert_eq!(transmission, vec![0.0, 0.5, 1.0]);
/// ```
pub fn smooth_step(x: &Vec<f64>, up_start: f64, up_end: f64, k: f64) -> Vec<f64> {
let m = (up_start + up_end) / 2.0;
x.iter().map(|&xi| 1.0 / (1.0 + E.powf(-k * (xi - m)))).collect()
}
/// Sigmoide step function for quadrupole selection simulation
///
/// Arguments:
///
/// * `x` - mz values
/// * `up_start` - start of the step up
/// * `up_end` - end of the step up
/// * `down_start` - start of the step down
/// * `down_end` - end of the step down
/// * `k` - steepness of the step
///
/// Returns:
///
/// * `Vec<f64>` - transmission probability for each mz value
///
/// # Examples
///
/// ```
/// use mscore::timstof::quadrupole::smooth_step_up_down;
///
/// let mz = vec![100.0, 200.0, 300.0];
/// let transmission = smooth_step_up_down(&mz, 150.0, 200.0, 250.0, 300.0, 0.5).iter().map(
/// |&x| (x * 100.0).round() / 100.0).collect::<Vec<f64>>();
/// assert_eq!(transmission, vec![0.0, 1.0, 0.0]);
/// ```
pub fn smooth_step_up_down(x: &Vec<f64>, up_start: f64, up_end: f64, down_start: f64, down_end: f64, k: f64) -> Vec<f64> {
let step_up = smooth_step(x, up_start, up_end, k);
let step_down = smooth_step(x, down_start, down_end, k);
step_up.iter().zip(step_down.iter()).map(|(&u, &d)| u - d).collect()
}
/// Ion transmission function for quadrupole selection simulation
///
/// Arguments:
///
/// * `midpoint` - center of the step
/// * `window_length` - length of the step
/// * `k` - steepness of the step
///
/// Returns:
///
/// * `impl Fn(Vec<f64>) -> Vec<f64>` - ion transmission function
///
/// # Examples
///
/// ```
/// use mscore::timstof::quadrupole::ion_transition_function_midpoint;
///
/// let ion_transmission = ion_transition_function_midpoint(150.0, 50.0, 1.0);
/// let mz = vec![100.0, 150.0, 170.0];
/// let transmission = ion_transmission(mz).iter().map(
/// |&x| (x * 100.0).round() / 100.0).collect::<Vec<f64>>();
/// assert_eq!(transmission, vec![0.0, 1.0, 1.0]);
/// ```
pub fn ion_transition_function_midpoint(midpoint: f64, window_length: f64, k: f64) -> impl Fn(Vec<f64>) -> Vec<f64> {
let half_window = window_length / 2.0;
let up_start = midpoint - half_window - 2.0;
let up_end = midpoint - half_window;
let down_start = midpoint + half_window;
let down_end = midpoint + half_window + 2.0;
// take a vector of mz values to their transmission probability
move |mz: Vec<f64>| -> Vec<f64> {
smooth_step_up_down(&mz, up_start, up_end, down_start, down_end, k)
}
}
/// Apply ion transmission function to mz values
///
/// Arguments:
///
/// * `midpoint` - center of the step
/// * `window_length` - length of the step
/// * `k` - steepness of the step
/// * `mz` - mz values
///
/// Returns:
///
/// * `Vec<f64>` - transmission probability for each mz value
///
/// # Examples
///
/// ```
/// use mscore::timstof::quadrupole::apply_transmission;
///
/// let mz = vec![100.0, 150.0, 170.0];
/// let transmission = apply_transmission(150.0, 50.0, 1.0, mz).iter().map(
/// |&x| (x * 100.0).round() / 100.0).collect::<Vec<f64>>();
/// assert_eq!(transmission, vec![0.0, 1.0, 1.0]);
/// ```
pub fn apply_transmission(midpoint: f64, window_length: f64, k: f64, mz: Vec<f64>) -> Vec<f64> {
ion_transition_function_midpoint(midpoint, window_length, k)(mz)
}
pub trait IonTransmission {
fn apply_transmission(&self, frame_id: i32, scan_id: i32, mz: &Vec<f64>) -> Vec<f64>;
/// Transmit a spectrum given a frame id and scan id
///
/// Arguments:
///
/// * `frame_id` - frame id
/// * `scan_id` - scan id
/// * `spectrum` - MzSpectrum
/// * `min_probability` - minimum probability for transmission
///
/// Returns:
///
/// * `MzSpectrum` - transmitted spectrum
///
fn transmit_spectrum(&self, frame_id: i32, scan_id: i32, spectrum: MzSpectrum, min_probability: Option<f64>) -> MzSpectrum {
let probability_cutoff = min_probability.unwrap_or(0.5);
let transmission_probability = self.apply_transmission(frame_id, scan_id, &spectrum.mz);
let mut filtered_mz = Vec::new();
let mut filtered_intensity = Vec::new();
// zip mz and intensity with transmission probability and filter out all mz values with transmission probability 0.001
for (i, (mz, intensity)) in spectrum.mz.iter().zip(spectrum.intensity.iter()).enumerate() {
if transmission_probability[i] > probability_cutoff {
filtered_mz.push(*mz);
filtered_intensity.push(*intensity* transmission_probability[i]);
}
}
MzSpectrum {
mz: filtered_mz,
intensity: filtered_intensity,
}
}
/// Transmit an annotated spectrum given a frame id and scan id
///
/// Arguments:
///
/// * `frame_id` - frame id
/// * `scan_id` - scan id
/// * `spectrum` - MzSpectrumAnnotated
/// * `min_probability` - minimum probability for transmission
///
/// Returns:
///
/// * `MzSpectrumAnnotated` - transmitted spectrum
///
fn transmit_annotated_spectrum(&self, frame_id: i32, scan_id: i32, spectrum: MzSpectrumAnnotated, min_probability: Option<f64>) -> MzSpectrumAnnotated {
let probability_cutoff = min_probability.unwrap_or(0.5);
let transmission_probability = self.apply_transmission(frame_id, scan_id, &spectrum.mz);
let mut filtered_mz = Vec::new();
let mut filtered_intensity = Vec::new();
let mut filtered_annotation = Vec::new();
// zip mz and intensity with transmission probability and filter out all mz values with transmission probability 0.5
for (i, (mz, intensity, annotation)) in izip!(spectrum.mz.iter(), spectrum.intensity.iter(), spectrum.annotations.iter()).enumerate() {
if transmission_probability[i] > probability_cutoff {
filtered_mz.push(*mz);
filtered_intensity.push(*intensity* transmission_probability[i]);
filtered_annotation.push(annotation.clone());
}
}
MzSpectrumAnnotated {
mz: filtered_mz,
intensity: filtered_intensity,
annotations: filtered_annotation,
}
}
fn transmit_ion(&self, frame_ids: Vec<i32>, scan_ids: Vec<i32>, spec: MzSpectrum, min_proba: Option<f64>) -> Vec<Vec<MzSpectrum>> {
let mut result: Vec<Vec<MzSpectrum>> = Vec::new();
for frame_id in frame_ids.iter() {
let mut frame_result: Vec<MzSpectrum> = Vec::new();
for scan_id in scan_ids.iter() {
let transmitted_spectrum = self.transmit_spectrum(*frame_id, *scan_id, spec.clone(), min_proba);
frame_result.push(transmitted_spectrum);
}
result.push(frame_result);
}
result
}
/// Get all ions in a frame that are transmitted
///
/// Arguments:
///
/// * `frame_id` - frame id
/// * `scan_id` - scan id
/// * `mz` - mz values
/// * `min_proba` - minimum probability for transmission
///
/// Returns:
///
/// * `HashSet<usize>` - indices of transmitted mz values
///
fn get_transmission_set(&self, frame_id: i32, scan_id: i32, mz: &Vec<f64>, min_proba: Option<f64>) -> HashSet<usize> {
// go over enumerated mz and push all indices with transmission probability > min_proba to a set
let probability_cutoff = min_proba.unwrap_or(0.5);
let transmission_probability = self.apply_transmission(frame_id, scan_id, mz);
mz.iter().enumerate().filter(|&(i, _)| transmission_probability[i] > probability_cutoff).map(|(i, _)| i).collect()
}
/// Check if all mz values in a given collection are transmitted
///
/// Arguments:
///
/// * `frame_id` - frame id
/// * `scan_id` - scan id
/// * `mz` - mz values
/// * `min_proba` - minimum probability for transmission
///
/// Returns:
///
/// * `bool` - true if all mz values are transmitted
///
fn all_transmitted(&self, frame_id: i32, scan_id: i32, mz: &Vec<f64>, min_proba: Option<f64>) -> bool {
let probability_cutoff = min_proba.unwrap_or(0.5);
let transmission_probability = self.apply_transmission(frame_id, scan_id, mz);
transmission_probability.iter().all(|&p| p > probability_cutoff)
}
/// Check if a single mz value is transmitted
///
/// Arguments:
///
/// * `frame_id` - frame id
/// * `scan_id` - scan id
/// * `mz` - mz value
/// * `min_proba` - minimum probability for transmission
///
/// Returns:
///
/// * `bool` - true if mz value is transmitted
///
fn is_transmitted(&self, frame_id: i32, scan_id: i32, mz: f64, min_proba: Option<f64>) -> bool {
let probability_cutoff = min_proba.unwrap_or(0.5);
let transmission_probability = self.apply_transmission(frame_id, scan_id, &vec![mz]);
transmission_probability[0] > probability_cutoff
}
/// Check if any mz value is transmitted, can be used to check if one peak of isotopic envelope is transmitted
///
/// Arguments:
///
/// * `frame_id` - frame id
/// * `scan_id` - scan id
/// * `mz` - mz values
/// * `min_proba` - minimum probability for transmission
///
/// Returns:
///
/// * `bool` - true if any mz value is transmitted
///
fn any_transmitted(&self, frame_id: i32, scan_id: i32, mz: &Vec<f64>, min_proba: Option<f64>) -> bool {
let probability_cutoff = min_proba.unwrap_or(0.5);
let transmission_probability = self.apply_transmission(frame_id, scan_id, mz);
transmission_probability.iter().any(|&p| p > probability_cutoff)
}
/// Transmit a frame given a diaPASEF transmission layout
fn transmit_tims_frame(&self, frame: &TimsFrame, min_probability: Option<f64>) -> TimsFrame {
let spectra = frame.to_tims_spectra();
let mut filtered_spectra = Vec::new();
for mut spectrum in spectra {
let filtered_spectrum = self.transmit_spectrum(frame.frame_id, spectrum.scan, spectrum.spectrum.mz_spectrum, min_probability);
if filtered_spectrum.mz.len() > 0 {
spectrum.spectrum.mz_spectrum = filtered_spectrum;
filtered_spectra.push(spectrum);
}
}
if filtered_spectra.len() > 0 {
TimsFrame::from_tims_spectra(filtered_spectra)
} else {
TimsFrame::new(
frame.frame_id,
frame.ms_type.clone(),
0.0,
vec![],
vec![],
vec![],
vec![],
vec![]
)
}
}
/// Transmit a frame given a diaPASEF transmission layout with annotations
///
/// Arguments:
///
/// * `frame` - TimsFrameAnnotated
/// * `min_probability` - minimum probability for transmission
///
/// Returns:
///
/// * `TimsFrameAnnotated` - transmitted frame
///
fn transmit_tims_frame_annotated(&self, frame: &TimsFrameAnnotated, min_probability: Option<f64>) -> TimsFrameAnnotated {
let spectra = frame.to_tims_spectra_annotated();
let mut filtered_spectra = Vec::new();
for mut spectrum in spectra {
let filtered_spectrum = self.transmit_annotated_spectrum(frame.frame_id, spectrum.scan as i32, spectrum.spectrum.clone(), min_probability);
if filtered_spectrum.mz.len() > 0 {
spectrum.spectrum = filtered_spectrum;
filtered_spectra.push(spectrum);
}
}
if filtered_spectra.len() > 0 {
TimsFrameAnnotated::from_tims_spectra_annotated(filtered_spectra)
} else {
TimsFrameAnnotated::new(
frame.frame_id,
frame.retention_time,
frame.ms_type.clone(),
vec![],
vec![],
vec![],
vec![],
vec![],
vec![]
)
}
}
fn isotopes_transmitted(&self, frame_id: i32, scan_id: i32, mz_mono: f64, isotopic_envelope: &Vec<f64>, min_probability: Option<f64>) -> (f64, Vec<(f64, f64)>) {
let probability_cutoff = min_probability.unwrap_or(0.5);
let transmission_probability = self.apply_transmission(frame_id, scan_id, &isotopic_envelope);
let mut result: Vec<(f64, f64)> = Vec::new();
for (mz, p) in isotopic_envelope.iter().zip(transmission_probability.iter()) {
if *p > probability_cutoff {
result.push((*mz - mz_mono, *p));
}
}
(mz_mono, result)
}
}
#[derive(Clone, Debug)]
pub struct TimsTransmissionDIA {
frame_to_window_group: HashMap<i32, i32>,
window_group_settings: HashMap<(i32, i32), (f64, f64)>,
k: f64,
}
impl TimsTransmissionDIA {
pub fn new(
frame: Vec<i32>,
frame_window_group: Vec<i32>,
window_group: Vec<i32>,
scan_start: Vec<i32>,
scan_end: Vec<i32>,
isolation_mz: Vec<f64>,
isolation_width: Vec<f64>,
k: Option<f64>,
) -> Self {
// hashmap from frame to window group
let frame_to_window_group = frame.iter().zip(frame_window_group.iter()).map(|(&f, &wg)| (f, wg)).collect::<HashMap<i32, i32>>();
let mut window_group_settings: HashMap<(i32, i32), (f64, f64)> = HashMap::new();
for (index, &wg) in window_group.iter().enumerate() {
let scan_start = scan_start[index];
let scan_end = scan_end[index];
let isolation_mz = isolation_mz[index];
let isolation_width = isolation_width[index];
let value = (isolation_mz, isolation_width);
for scan in scan_start..scan_end + 1 {
let key = (wg, scan);
window_group_settings.insert(key, value);
}
}
Self {
frame_to_window_group,
window_group_settings,
k: k.unwrap_or(2.0),
}
}
pub fn frame_to_window_group(&self, frame_id: i32) -> i32 {
let window_group = self.frame_to_window_group.get(&frame_id);
match window_group {
Some(&wg) => wg,
None => -1,
}
}
pub fn get_setting(&self, window_group: i32, scan_id: i32) -> Option<&(f64, f64)> {
let setting = self.window_group_settings.get(&(window_group, scan_id));
match setting {
Some(s) => Some(s),
None => None,
}
}
// check if a frame is a precursor frame
pub fn is_precursor(&self, frame_id: i32) -> bool {
// if frame id is in the hashmap, it is not a precursor frame
match self.frame_to_window_group.contains_key(&frame_id) {
true => false,
false => true,
}
}
}
impl IonTransmission for TimsTransmissionDIA {
fn apply_transmission(&self, frame_id: i32, scan_id: i32, mz: &Vec<f64>) -> Vec<f64> {
let setting = self.get_setting(self.frame_to_window_group(frame_id), scan_id);
let is_precursor = self.is_precursor(frame_id);
match setting {
Some((isolation_mz, isolation_width)) => {
apply_transmission(*isolation_mz, *isolation_width, self.k, mz.clone())
},
None => match is_precursor {
true => vec![1.0; mz.len()],
false => vec![0.0; mz.len()],
}
}
}
}