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beta-relea
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dev
| Author | SHA1 | Date |
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 Emilia Allison
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f50db96697
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32
README.md
32
README.md
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@ -51,7 +51,7 @@ However, it is much easier to click-and-drag the desired region.
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If we click and hold on a well (see right pane), that specifies our start well.
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If we click and hold on a well (see right pane), that specifies our start well.
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Then, we can drag and subsequently release on our desired end well.
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Then, we can drag and subsequently release on our desired end well.
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Our selected wells will be bolded (thicker outline).
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Our selected wells will be highlighted in light blue for our source plate and light red for our destination plate.
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You might also notice that some wells are hatched:
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You might also notice that some wells are hatched:
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this indicates wells that will be used in the transfer.
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this indicates wells that will be used in the transfer.
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Not all selected wells will necessarily be hatched,
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Not all selected wells will necessarily be hatched,
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@ -68,29 +68,6 @@ When finished, click the "Save" button to commit these changes.
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If you no longer need a transfer, select it as above and then click the "Delete" button.
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If you no longer need a transfer, select it as above and then click the "Delete" button.
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#### Interleave
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Interleave can be set for both source and destination plates.
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Essentially, it can be read as "use every Nth well".
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That is, a source row interleave of 2 would use every other row of the selected region.
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It is permitted to have interleave in both dimensions on both plates in a single transfer.
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#### Pooling
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Consider a case where you want to condense an entire column in a source plate into just one row in the destination.
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Instead of creating multiple transfers, it is sufficient to set the destination row interleave to 0.
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An 0 interleave can be thought of as condensing that dimension to a point.
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For this reason, 0 interleaves are not permitted on source plates (consider what this would represent).
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Similarly, 0 interleaves are not permitted in replicate transfers (see next section).
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#### Replicates
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Where pooling permits a "many-to-one" transfer, replicates are "one-to-many".
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This behavior is achieved by selecting a region in the destination plate instead of just a plate.
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(If the corners of the destination region are not identical, it is a replicate.)
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Plate-tool will attempt to fit as many copies into the selected destination region as space permits.
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Partial copies will not be created.
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That is, if a source region is 3 wells wide and a destination region is 7 wells wide,
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2 copies will be made, and the 7th well in the destination will be left unused.
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### Importing and Exporting
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### Importing and Exporting
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#### Export as CSV
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#### Export as CSV
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@ -224,10 +201,3 @@ Here's how:
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- You may need to check where `cargo` is installing binaries by default. For me, they're at `~/.cargo/bin`.
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- You may need to check where `cargo` is installing binaries by default. For me, they're at `~/.cargo/bin`.
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If trunk is not automatically placed in your path, you would then run `/your/path/to/.cargo/bin/trunk serve`.
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If trunk is not automatically placed in your path, you would then run `/your/path/to/.cargo/bin/trunk serve`.
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- You can instead run `trunk build --release` for a more performant binary.
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- You can instead run `trunk build --release` for a more performant binary.
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## Bug Reports and Further Help
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Any requests for help or assistance with bugs can be sent to platetool(at)ilia.moe
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If reporting a bug, ideally include what it was you were trying to do and, if possible, a screenshot or any logs in
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your browser's console.
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@ -182,61 +182,98 @@ impl TransferRegion {
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let Well { row: i, col: j } = w;
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let Well { row: i, col: j } = w;
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if source_wells.contains(&w) {
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if source_wells.contains(&w) {
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let possible_destination_wells = create_dense_rectangle(c1, c2);
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let possible_destination_wells = create_dense_rectangle(c1, c2);
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// Destination upper-left, bottom-right
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let (d_ul, d_br) = standardize_rectangle(c1, c2);
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let (d_ul, d_br) = standardize_rectangle(c1, c2);
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// Source upper-left, bottom-right
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let (s_ul, s_br) =
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let (s_ul, s_br) =
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standardize_rectangle(&source_corners.0, &source_corners.1);
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standardize_rectangle(&source_corners.0, &source_corners.1);
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// Get base size of source region before interleave
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let s_dims = (
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let s_dims = (
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s_br.row.checked_sub(s_ul.row).unwrap() + 1,
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s_br.row.checked_sub(s_ul.row).unwrap() + 1,
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s_br.col.checked_sub(s_ul.col).unwrap() + 1,
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s_br.col.checked_sub(s_ul.col).unwrap() + 1,
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);
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);
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// Get base size of destination region before interleave
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let d_dims = (
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let d_dims = (
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d_br.row.checked_sub(d_ul.row).unwrap() + 1,
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d_br.row.checked_sub(d_ul.row).unwrap() + 1,
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d_br.col.checked_sub(d_ul.col).unwrap() + 1,
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d_br.col.checked_sub(d_ul.col).unwrap() + 1,
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);
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);
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// Precompute unsigned_abs: this should be cheap but
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// this is called constantly in loops, plus prettier this way
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let il_dest_uabs = (il_dest.0.unsigned_abs(), il_dest.1.unsigned_abs());
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let il_source_uabs = (il_source.0.unsigned_abs(), il_source.1.unsigned_abs());
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// Get the actual number of source wells in each dimension
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// after considering interleave; essentially squish the air out of the
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// region.
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let number_used_src_wells = (
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let number_used_src_wells = (
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// Number of used source wells
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(s_dims.0 + il_source_uabs.0 - 1)
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(s_dims.0 + il_source.0.unsigned_abs() - 1)
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.div_euclid(il_source_uabs.0),
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.div_euclid(il_source.0.unsigned_abs()),
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(s_dims.1 + il_source_uabs.1 - 1)
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(s_dims.1 + il_source.1.unsigned_abs() - 1)
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.div_euclid(il_source_uabs.1),
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.div_euclid(il_source.1.unsigned_abs()),
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);
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);
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let count = (
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// How many times can we replicate?
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// How many times can we replicate in each direction?
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if il_dest.0.unsigned_abs() == 0 {
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// Lazy solution: just increment the number of replicates until it wouldn't
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// fit anymore!
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let count = {
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let replicate_base_size = (
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number_used_src_wells.0 * il_dest_uabs.0,
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number_used_src_wells.1 * il_dest_uabs.1,
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);
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(
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if il_dest_uabs.0 == 0 {
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1
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1
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} else {
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} else {
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(1..)
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(1..)
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.position(|n| {
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.position(|n| {
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(n * number_used_src_wells.0 * il_dest.0.unsigned_abs())
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(n * replicate_base_size.0)
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.saturating_sub(il_dest.0.unsigned_abs())
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.saturating_sub(il_dest_uabs.0)
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+ 1
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+ 1
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> d_dims.0
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> d_dims.0
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})
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})
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.unwrap() as u8
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.unwrap() as u8
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},
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},
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if il_dest.1.unsigned_abs() == 0 {
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if il_dest_uabs.1 == 0 {
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1
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1
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} else {
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} else {
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(1..)
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(1..)
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.position(|n| {
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.position(|n| {
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(n * number_used_src_wells.1 * il_dest.1.unsigned_abs())
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(n * replicate_base_size.1)
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.saturating_sub(il_dest.1.unsigned_abs())
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.saturating_sub(il_dest_uabs.1)
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+ 1
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+ 1
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> d_dims.1
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> d_dims.1
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})
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})
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.unwrap() as u8
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.unwrap() as u8
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},
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},
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);
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)
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};
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// Normalize our i,j (source coords) to a dense rectangle consisting only
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// of points actually in the transfer.
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let i = i
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let i = i
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.saturating_sub(s_ul.row)
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.saturating_sub(s_ul.row)
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.saturating_div(il_source.0.unsigned_abs());
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.saturating_div(il_source_uabs.0);
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let j = j
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let j = j
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.saturating_sub(s_ul.col)
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.saturating_sub(s_ul.col)
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.saturating_div(il_source.1.unsigned_abs());
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.saturating_div(il_source_uabs.1);
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let checked_il_dest = (u8::max(il_dest.0.unsigned_abs(), 1u8),
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u8::max(il_dest.1.unsigned_abs(), 1u8));
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// Should not matter because of validation,
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// but a cheap way to prevent div by 0
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let checked_il_dest = (
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u8::max(il_dest_uabs.0, 1u8),
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u8::max(il_dest_uabs.1, 1u8),
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);
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// Precompute multiplication
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let row_modulus = number_used_src_wells.0 * checked_il_dest.0;
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let row_modulus = number_used_src_wells.0 * checked_il_dest.0;
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let column_modulus = number_used_src_wells.1 * checked_il_dest.1;
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let column_modulus = number_used_src_wells.1 * checked_il_dest.1;
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let residue_class = (
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(il_dest_uabs.0 * i) % row_modulus,
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(il_dest_uabs.1 * j) % column_modulus
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);
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Some(
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Some(
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possible_destination_wells
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possible_destination_wells
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@ -244,24 +281,22 @@ impl TransferRegion {
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.filter(|Well { row: x, .. }| {
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.filter(|Well { row: x, .. }| {
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x.checked_sub(d_ul.row).unwrap()
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x.checked_sub(d_ul.row).unwrap()
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% row_modulus // Counter along x
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% row_modulus // Counter along x
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== (il_dest.0.unsigned_abs() *i)
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== residue_class.0
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% row_modulus
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})
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})
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.filter(|Well { col: y, .. }| {
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.filter(|Well { col: y, .. }| {
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y.checked_sub(d_ul.col).unwrap()
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y.checked_sub(d_ul.col).unwrap()
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% column_modulus // Counter along u
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% column_modulus // Counter along u
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== (il_dest.1.unsigned_abs() *j)
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== residue_class.1
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% column_modulus
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})
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})
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.filter(|Well { row: x, col: y }| {
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.filter(|Well { row: x, col: y }| {
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// How many times have we replicated? < How many are we allowed
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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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// to replicate?
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x.checked_sub(d_ul.row).unwrap().div_euclid(
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x.checked_sub(d_ul.row).unwrap().div_euclid(row_modulus)
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row_modulus
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< count.0
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) < count.0
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&& y.checked_sub(d_ul.col)
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&& y.checked_sub(d_ul.col).unwrap().div_euclid(
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.unwrap()
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column_modulus
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.div_euclid(column_modulus)
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) < count.1
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< count.1
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})
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})
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.collect(),
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.collect(),
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)
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)
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@ -319,8 +354,8 @@ impl TransferRegion {
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return Err("Source region is out-of-bounds! (Too wide)");
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return Err("Source region is out-of-bounds! (Too wide)");
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}
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}
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if il_dest == (0,0) {
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if il_dest == (0, 0) {
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return Err("Refusing to pool both dimensions in a rectangular transfer!\nPlease select a point in the destination plate.")
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return Err("Refusing to pool both dimensions in a rectangular transfer!\nPlease select a point in the destination plate.");
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}
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}
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}
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}
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Region::Custom(_) => return Ok(()),
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Region::Custom(_) => return Ok(()),
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@ -343,7 +378,8 @@ fn create_dense_rectangle(c1: &Well, c2: &Well) -> Vec<Well> {
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// Creates a vector of every point between two corners
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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 (c1, c2) = standardize_rectangle(c1, c2);
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let mut points = Vec::<Well>::new();
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let number_wells: usize = ((c2.row - c1.row + 1) as usize) * ((c2.col - c1.col + 1) as usize);
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let mut points = Vec::<Well>::with_capacity(number_wells);
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for i in c1.row..=c2.row {
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for i in c1.row..=c2.row {
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for j in c1.col..=c2.col {
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for j in c1.col..=c2.col {
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points.push(Well { row: i, col: j });
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points.push(Well { row: i, col: j });
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