442 lines
18 KiB
Rust
442 lines
18 KiB
Rust
use serde::{Serialize, Deserialize};
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use super::plate::Plate;
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#[derive(Clone, Copy, PartialEq, Eq, Serialize, Deserialize, Debug)]
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pub enum Region {
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Rect((u8, u8), (u8, u8)),
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Point((u8, u8)),
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}
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impl Default for Region {
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fn default() -> Self {
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Region::Point((1,1))
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}
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}
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impl TryFrom<Region> for ((u8, u8), (u8, u8)) {
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type Error = &'static str;
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fn try_from(region: Region) -> Result<Self, Self::Error> {
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if let Region::Rect(c1, c2) = region {
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Ok((c1, c2))
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} else {
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// Should consider returning a degenerate rectangle here instead
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Err("Cannot convert this region to a rectangle, it was a point.")
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}
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}
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}
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#[derive(PartialEq, Eq, Clone, Copy, Serialize, Deserialize, Debug)]
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pub struct TransferRegion {
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pub source_plate: Plate,
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pub source_region: Region, // Even if it is just a point, we don't want corners.
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pub dest_plate: Plate,
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pub dest_region: Region,
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pub interleave_source: (i8, i8),
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pub interleave_dest: (i8, i8),
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}
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impl Default for TransferRegion {
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fn default() -> Self {
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TransferRegion {
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source_plate: Plate::default(),
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source_region: Region::default(),
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dest_plate: Plate::default(),
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dest_region: Region::default(),
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interleave_source: (1,1),
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interleave_dest: (1,1)
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}
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}
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}
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impl TransferRegion {
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pub fn get_source_wells(&self) -> Vec<(u8, u8)> {
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match self.source_region {
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Region::Rect(c1, c2) => {
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let mut wells = Vec::<(u8, u8)>::new();
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let (ul, br) = standardize_rectangle(&c1, &c2);
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let (interleave_i, interleave_j) = self.interleave_source;
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// NOTE: This will panic if either is 0!
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// We'll reassign these values (still not mutable) just in case.
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// This behaviour shouldn't be replicated for destination wells
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// because a zero step permits pooling.
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let (interleave_i, interleave_j) = (i8::max(interleave_i, 1), i8::max(interleave_j, 1));
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for i in (ul.0..=br.0).step_by(i8::abs(interleave_i) as usize) {
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for j in (ul.1..=br.1).step_by(i8::abs(interleave_j) as usize) {
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// NOTE: It looks like we're ignoring negative interleaves,
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// because it wouldn't make a difference here---the same
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// wells will still be involved in the transfer.
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wells.push((i, j))
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}
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}
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return wells;
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},
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Region::Point(p) => return vec![p]
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}
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}
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pub fn get_destination_wells(&self) -> Vec<(u8, u8)> {
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let map = self.calculate_map();
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let source_wells = self.get_source_wells();
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let mut wells = Vec::<(u8, u8)>::new();
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log::debug!("GDW:");
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for well in source_wells {
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if let Some(mut dest_wells) = map(well) {
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log::debug!("Map {:?} to {:?}", well, dest_wells);
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wells.append(&mut dest_wells);
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}
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}
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log::debug!("GDW END.");
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return wells;
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}
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pub fn calculate_map(&self) -> Box<dyn Fn((u8, u8)) -> Option<Vec<(u8, u8)>> + '_> {
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// By validating first, we have a stronger guarantee that
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// this function will not panic. :)
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log::debug!("Validating: {:?}", self.validate());
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if let Err(msg) = self.validate() {
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eprintln!("{}", msg);
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eprintln!("This transfer will be empty.");
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return Box::new(|(_, _)| None);
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}
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log::debug!("What is ild? {:?}", self);
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let source_wells = self.get_source_wells();
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let il_dest = self.interleave_dest;
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let il_source = self.interleave_source;
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let source_corners: ((u8, u8), (u8, u8)) = match self.source_region {
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Region::Point((x,y)) => ((x,y),(x,y)),
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Region::Rect(c1,c2) => (c1,c2)
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};
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let (source_ul, _) = standardize_rectangle(&source_corners.0, &source_corners.1);
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// This map is not necessarily injective or surjective,
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// but we will have these properties in certain cases.
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// If the transfer is not a pooling transfer (interleave == 0)
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// and simple then we *will* have injectivity.
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// Non-replicate transfers:
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match self.dest_region {
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Region::Point((x, y)) => {
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return Box::new(move |(i, j)| {
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if source_wells.contains(&(i, j)) {
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// Validity here already checked by self.validate()
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Some(vec![(
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x + i
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.checked_sub(source_ul.0)
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.expect("Point cannot have been less than UL")
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.checked_div(il_source.0.abs() as u8)
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.expect("Source interleave cannot be 0")
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.mul(il_dest.0.abs() as u8),
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y + j
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.checked_sub(source_ul.1)
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.expect("Point cannot have been less than UL")
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.checked_div(il_source.1.abs() as u8)
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.expect("Source interleave cannot be 0")
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.mul(il_dest.1.abs() as u8),
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)])
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} else {
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None
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}
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});
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}
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Region::Rect(c1, c2) => {
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return Box::new(move |(i, j)| {
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if source_wells.contains(&(i, j)) {
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let possible_destination_wells = create_dense_rectangle(&c1, &c2);
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let (d_ul, d_br) = standardize_rectangle(&c1, &c2);
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let (s_ul, s_br) = standardize_rectangle(&source_corners.0, &source_corners.1);
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let s_dims = (
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s_br.0.checked_sub(s_ul.0).unwrap() + 1,
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s_br.1.checked_sub(s_ul.1).unwrap() + 1,
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);
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let d_dims = (
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d_br.0.checked_sub(d_ul.0).unwrap() + 1,
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d_br.1.checked_sub(d_ul.1).unwrap() + 1,
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);
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let N_s = ( // Number of used source wells
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(s_dims.0 + il_source.0.abs() as u8 - 1).div_euclid(il_source.0.abs() as u8),
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(s_dims.1 + il_source.1.abs() as u8 - 1).div_euclid(il_source.1.abs() as u8),
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);
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let D_per_replicate = ( // How many wells are used per replicate?
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(N_s.0 * (il_dest.0.abs() as u8))
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// Conditionally subtract one to ignore the trailing interleave well
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.saturating_sub(if il_dest.0.abs() > 1 {1} else {0}),
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(N_s.1 * (il_dest.1.abs() as u8))
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.saturating_sub(if il_dest.1.abs() > 1 {1} else {0}),
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);
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let count = ( // How many times can we replicate?
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d_dims.0.div_euclid(D_per_replicate.0),
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d_dims.1.div_euclid(D_per_replicate.1),
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);
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let i = i.saturating_sub(s_ul.0).saturating_div(il_source.0.abs() as u8);
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let j = j.saturating_sub(s_ul.1).saturating_div(il_source.1.abs() as u8);
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log::debug!("s_dims: {:?}, N_s: {:?}", s_dims, N_s);
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Some(
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possible_destination_wells
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.into_iter()
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.filter(|(x, _)| {
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x.checked_sub(d_ul.0).unwrap()
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% (N_s.0 * il_dest.0.abs() as u8) // Counter along x
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== ((il_dest.0.abs() as u8 *i))
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% (N_s.0 * il_dest.0.abs() as u8)
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})
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.filter(|(_, y)| {
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y.checked_sub(d_ul.1).unwrap()
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% (N_s.1 * il_dest.1.abs() as u8) // Counter along u
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== ((il_dest.1.abs() as u8 *j))
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% (N_s.1 * il_dest.1.abs() as u8)
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})
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.filter(|(x,y)| {
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// How many times have we replicated? < How many are we allowed
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// to replicate?
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x.checked_sub(d_ul.0).unwrap().div_euclid(N_s.0 * il_dest.0.abs() as u8)
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< count.0 &&
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y.checked_sub(d_ul.1).unwrap().div_euclid(N_s.1 * il_dest.1.abs() as u8)
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< count.1
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})
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.collect(),
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)
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} else {
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None
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}
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});
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}
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}
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}
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pub fn validate(&self) -> Result<(), &'static str> {
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// Checks if the region does anything suspect
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//
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// If validation fails, we pass a string to show to the user.
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//
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// We check:
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// - Are the wells in the source really there?
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// - In a replication region, do the source lengths divide the destination lengths?
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// - Are the interleaves valid?
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let il_source = self.interleave_source;
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let il_dest = self.interleave_dest;
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match self.source_region {
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Region::Point(_) => return Ok(()), // Should make sure it's actually in the plate, leave for
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// later
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Region::Rect(s1, s2) => {
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// Check if all source wells exist:
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if s1.0 == 0 || s1.1 == 0 || s2.0 == 0 || s2.1 == 0 {
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return Err("Source region is out-of-bounds! (Too small)");
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}
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// Sufficient to check if the corners are in-bounds
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let source_max = self.source_plate.size();
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if s1.0 > source_max.0 || s2.0 > source_max.0 {
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return Err("Source region is out-of-bounds! (Too tall)");
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}
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if s1.1 > source_max.1 || s2.1 > source_max.1 {
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log::debug!("s1.1: {}, max.1: {}", s1.1, source_max.1);
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return Err("Source region is out-of-bounds! (Too wide)");
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}
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// Check that source lengths divide destination lengths
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/* This section is disabled because it's not
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* strictly necessary to have this property (divisibility)
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match &self.dest_region {
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Region::Point(_) => (),
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Region::Rect(d1, d2) => {
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// If we consider interleaves, it's slightly more
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// complicated to compute the true dimensions of
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// each region.
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// (dim)*(il) - (il - 1)
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let dest_dim_i = u8::abs_diff(d1.0, d2.0)+1;
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let dest_dim_j = u8::abs_diff(d1.1, d2.1)+1;
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let source_dim_i = ((il_source.0.abs() as u8) * u8::abs_diff(s1.0, s2.0))
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.checked_sub(il_source.0.abs() as u8 - 1)
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.expect("Dimension is somehow negative?")
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+ 1;
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let source_dim_j = ((il_source.1.abs() as u8) * u8::abs_diff(s1.1, s2.1))
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.checked_sub(il_source.1.abs() as u8 - 1)
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.expect("Dimension is somehow negative?")
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+ 1;
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if dest_dim_i % (source_dim_i+il_dest.0.abs() as u8) != 0 {
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eprintln!("{} % {} = {}", dest_dim_i,
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source_dim_i+il_dest.0.abs() as u8,
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dest_dim_i % (source_dim_i+il_dest.0.abs() as u8));
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return Err("Replicate region has indivisible height!");
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}
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if dest_dim_j % (source_dim_j+il_dest.1.abs() as u8) != 0 {
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eprintln!("{} {}", source_dim_j, source_dim_j);
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return Err("Replicate region has indivisible width!");
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}
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}
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}
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*/
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}
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}
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if il_source.0 == 0 || il_dest.1 == 0 {
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return Err("Source interleave cannot be zero!");
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}
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// Check if all destination wells exist:
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// NOT IMPLEMENTED
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// Should *not* happen in this function---otherwise
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// we'd get a nasty recursive loop.
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return Ok(());
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}
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}
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fn in_region(pt: (u8, u8), r: &Region) -> bool {
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match r {
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Region::Rect(c1, c2) => {
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pt.0 <= u8::max(c1.0, c2.0)
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&& pt.0 >= u8::min(c1.0, c2.0)
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&& pt.1 <= u8::max(c1.1, c2.1)
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&& pt.1 >= u8::min(c1.1, c2.1)
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}
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Region::Point((i, j)) => pt.0 == *i && pt.1 == *j,
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}
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}
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fn create_dense_rectangle(c1: &(u8, u8), c2: &(u8, u8)) -> Vec<(u8, u8)> {
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// Creates a vector of every point between two corners
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let (c1, c2) = standardize_rectangle(c1, c2);
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let mut points = Vec::<(u8, u8)>::new();
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for i in c1.0..=c2.0 {
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for j in c1.1..=c2.1 {
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points.push((i, j));
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}
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}
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return points;
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}
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fn standardize_rectangle(c1: &(u8, u8), c2: &(u8, u8)) -> ((u8, u8), (u8, u8)) {
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let upper_left_i = u8::min(c1.0, c2.0);
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let upper_left_j = u8::min(c1.1, c2.1);
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let bottom_right_i = u8::max(c1.0, c2.0);
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let bottom_right_j = u8::max(c1.1, c2.1);
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return (
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(upper_left_i, upper_left_j),
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(bottom_right_i, bottom_right_j),
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);
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}
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#[cfg(debug_assertions)]
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use std::fmt;
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use std::ops::Mul;
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#[cfg(debug_assertions)] // There should be no reason to print a transfer otherwise
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impl fmt::Display for TransferRegion {
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fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
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writeln!(f, "Source Plate:")?;
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let source_dims = self.source_plate.size();
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let source_wells = self.get_source_wells();
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let mut source_string = String::new();
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for i in 1..=source_dims.0 {
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for j in 1..=source_dims.1 {
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if source_wells.contains(&(i, j)) {
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source_string.push_str("x")
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} else {
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source_string.push_str(".")
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}
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}
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source_string.push_str("\n");
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}
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write!(f, "{}", source_string)?;
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writeln!(f, "Dest Plate:")?;
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let dest_dims = self.dest_plate.size();
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let dest_wells = self.get_destination_wells();
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let mut dest_string = String::new();
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for i in 1..=dest_dims.0 {
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for j in 1..=dest_dims.1 {
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if dest_wells.contains(&(i, j)) {
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dest_string.push_str("x")
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} else {
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dest_string.push_str(".")
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}
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}
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dest_string.push_str("\n");
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}
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write!(f, "{}", dest_string)
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}
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}
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#[cfg(test)]
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mod tests {
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use crate::data::plate::*;
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use crate::data::transfer_region::*;
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#[test]
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fn test_simple_transfer() {
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let source = Plate::new(PlateType::Source, PlateFormat::W96);
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let destination = Plate::new(PlateType::Destination, PlateFormat::W384);
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let transfer1 = TransferRegion {
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source_plate: source,
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source_region: Region::Rect((1, 1), (3, 3)),
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dest_plate: destination,
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dest_region: Region::Point((3,3)),
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interleave_source: (1,1),
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interleave_dest: (1,1),
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};
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let transfer1_map = transfer1.calculate_map();
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assert_eq!(transfer1_map((1,1)), Some(vec!{(3,3)}), "Failed basic shift transfer 1");
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assert_eq!(transfer1_map((1,2)), Some(vec!{(3,4)}), "Failed basic shift transfer 2");
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assert_eq!(transfer1_map((2,2)), Some(vec!{(4,4)}), "Failed basic shift transfer 3");
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let transfer2 = TransferRegion {
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source_plate: source,
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source_region: Region::Rect((1, 1), (3, 3)),
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dest_plate: destination,
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dest_region: Region::Point((3,3)),
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interleave_source: (2,2),
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interleave_dest: (1,1),
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};
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let transfer2_map = transfer2.calculate_map();
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assert_eq!(transfer2_map((1,1)), Some(vec!{(3,3)}), "Failed source interleave, type simple 1");
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assert_eq!(transfer2_map((1,2)), None, "Failed source interleave, type simple 2");
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assert_eq!(transfer2_map((2,2)), None, "Failed source interleave, type simple 3");
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assert_eq!(transfer2_map((3,3)), Some(vec!{(4,4)}), "Failed source interleave, type simple 4");
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let transfer3 = TransferRegion {
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source_plate: source,
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source_region: Region::Rect((1, 1), (3, 3)),
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dest_plate: destination,
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dest_region: Region::Point((3,3)),
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interleave_source: (1,1),
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interleave_dest: (2,3),
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};
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let transfer3_map = transfer3.calculate_map();
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assert_eq!(transfer3_map((1,1)), Some(vec!{(3,3)}), "Failed destination interleave, type simple 1");
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assert_eq!(transfer3_map((2,1)), Some(vec!{(5,3)}), "Failed destination interleave, type simple 2");
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assert_eq!(transfer3_map((1,2)), Some(vec!{(3,6)}), "Failed destination interleave, type simple 3");
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assert_eq!(transfer3_map((2,2)), Some(vec!{(5,6)}), "Failed destination interleave, type simple 4");
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}
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#[test]
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fn test_replicate_transfer() {
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let source = Plate::new(PlateType::Source, PlateFormat::W96);
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let destination = Plate::new(PlateType::Destination, PlateFormat::W384);
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let transfer1 = TransferRegion {
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source_plate: source,
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source_region: Region::Rect((1, 1), (2, 2)),
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dest_plate: destination,
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dest_region: Region::Rect((2,2),(11,11)),
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interleave_source: (1,1),
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interleave_dest: (3,3),
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};
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let transfer1_map = transfer1.calculate_map();
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assert_eq!(transfer1_map((1,1)), Some(vec!{(2, 2), (2, 8), (8, 2), (8, 8)}), "Failed type replicate 1");
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assert_eq!(transfer1_map((2,1)), Some(vec!{(5, 2), (5, 8), (11, 2), (11, 8)}), "Failed type replicate 1");
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}
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#[test]
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fn test_pooling_transfer() {
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}
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}
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