use super::run_squeeze_if_needed;
use crate::convert::{build_from_zarr_matrix, MatrixLayout};
use crate::sparse_io::*;
use crate::sparse_util::*;
use crate::zarr_io::*;
use log::info;
#[derive(clap::Args, Debug)]
pub struct FromZarrArgs {
#[arg(
help = "Input Zarr file containing sparse matrix triplets",
long_help = "Specify the Zarr file where triplets of sparse matrix data are stored.\n\
For example, 10X Genomics Xenium's 'cell_feature_matrix.zarr.zip'."
)]
pub zarr_file: Box<str>,
#[arg(
long,
value_enum,
default_value = "zarr",
help = "Backend format for output",
long_help = "Choose the backend format for the output file.\n\
Supported formats include 'zarr' and 'h5'."
)]
pub backend: SparseIoBackend,
#[arg(
short,
long,
help = "Output file header or name",
long_help = "Specify the output file header.\n\
The zarr backend produces {output}.zarr.zip by default;\n\
pass --no-zip to keep a {output}.zarr directory instead.\n\
Redundant {backend} names will be ignored."
)]
pub output: Box<str>,
#[arg(long = "no-zip", default_value_t = true, action = clap::ArgAction::SetFalse)]
pub zip: bool,
#[arg(
short = 'd',
long,
default_value = MatrixLayout::XENIUM_DATA,
help = "Data field path",
long_help = "Path to the dataset containing triplet values.\n\
Use the 'list-zarr' subcommand to inspect available fields."
)]
pub data_field: Box<str>,
#[arg(
short = 'i',
long,
default_value = MatrixLayout::XENIUM_INDICES,
help = "Indices field path",
long_help = "Path to the dataset containing indices. Row indices for CSC,\n\
column indices for CSR."
)]
pub indices_field: Box<str>,
#[arg(
short = 'p',
long,
default_value = MatrixLayout::XENIUM_INDPTR,
help = "Indptr field path",
long_help = "Path to the dataset containing indptr. Column pointers for CSC,\n\
row pointers for CSR."
)]
pub indptr_field: Box<str>,
#[arg(
short = 't',
long,
value_enum,
default_value = "row",
help = "Pointer type (row or column)",
long_help = "Specify whether the pointers keep track of row (gene) or column (cell) indices."
)]
pub pointer_type: IndexPointerType,
#[arg(
short = 'r',
long,
default_value = MatrixLayout::XENIUM_ROW_IDS,
help = "Row ID field path",
long_help = "Path to the group or dataset for row, gene, or feature IDs."
)]
pub row_id_field: Box<str>,
#[arg(
short = 'n',
long,
default_value = MatrixLayout::XENIUM_ROW_NAMES,
help = "Row name field path",
long_help = "Path to the group or dataset for row, gene, or feature names."
)]
pub row_name_field: Box<str>,
#[arg(
short = 'f',
long,
default_value = MatrixLayout::XENIUM_ROW_TYPES,
help = "Row type field path",
long_help = "Path to the group or dataset for row, gene, or feature types."
)]
pub row_type_field: Box<str>,
#[arg(
long,
default_value = MatrixLayout::SELECT_ROW_TYPES,
help = "Select row type (comma-separated patterns; ANY match keeps the row)",
long_help = "Select which row types to include. Patterns are comma-separated,\n\
case-insensitive substrings.\n\
A row is kept if its type contains any pattern.\n\
The default 'gene,peak' keeps Gene Expression and ATAC Peaks."
)]
pub select_row_type: Box<str>,
#[arg(
long,
default_value = MatrixLayout::REMOVE_ROW_TYPES,
help = "Remove row type (comma-separated patterns; ANY match drops the row)",
long_help = "Remove rows if their type contains any of these comma-separated patterns."
)]
pub remove_row_type: Box<str>,
#[arg(
short = 'c',
long,
default_value = MatrixLayout::XENIUM_COLUMN_NAMES,
help = "Column name field path",
long_help = "Path to the group or dataset for columns or cells.\n\
Will first attempt Xenium's Cell ID format mapping."
)]
pub column_name_field: Box<str>,
#[arg(
long,
default_value_t = false,
help = "Squeeze sparse rows or columns",
long_help = "Enable squeezing to remove rows and columns with too few non-zeros.\n\
This can help reduce file size and improve performance."
)]
pub do_squeeze: bool,
#[arg(
long,
default_value_t = 1,
help = "Row non-zero cutoff",
long_help = "Minimum number of non-zero elements required for rows.\n\
Rows with fewer non-zeros will be removed if squeezing is enabled."
)]
pub row_nnz_cutoff: usize,
#[arg(
long,
default_value_t = 1,
help = "Column non-zero cutoff",
long_help = "Minimum number of non-zero elements required for columns.\n\
Columns with fewer non-zeros will be removed if squeezing is enabled."
)]
pub column_nnz_cutoff: usize,
#[arg(
long,
help = "Cells per rayon job for the post-build squeeze pass",
long_help = "Cells per rayon job for the post-build squeeze pass.\n\
Omit it for auto-scaling by feature count."
)]
pub block_size: Option<usize>,
}
pub fn run_build_from_zarr_triplets(args: &FromZarrArgs) -> anyhow::Result<()> {
let (effective_output, backend, backend_file) =
prepare_output(&args.output, args.backend.clone(), args.zip)?;
let layout = MatrixLayout {
data_field: args.data_field.clone(),
indices_field: args.indices_field.clone(),
indptr_field: args.indptr_field.clone(),
pointer_type: args.pointer_type,
row_id_field: args.row_id_field.clone(),
row_name_field: args.row_name_field.clone(),
row_type_field: args.row_type_field.clone(),
select_row_type: args.select_row_type.clone(),
remove_row_type: args.remove_row_type.clone(),
column_name_field: args.column_name_field.clone(),
};
build_from_zarr_matrix(&args.zarr_file, &layout, &backend_file, &backend)?;
run_squeeze_if_needed(
args.do_squeeze,
args.row_nnz_cutoff,
args.column_nnz_cutoff,
args.block_size,
&backend_file,
)?;
finalize_output(&backend_file, &effective_output)?;
info!("done");
Ok(())
}