Exporting Data

CSV

Available with the default csv feature.

#![allow(unused)]
fn main() {
use biodream::{CsvOptions, TimeFormat};

let df = biodream::read_file("recording.acq")?.into_value();

let opts = CsvOptions {
    time_format: TimeFormat::Seconds,
    include_markers: true,
    delimiter: b',',
};

df.to_csv("output.csv", &opts)?;
}

TimeFormat

Multi-rate channels in CSV

When channels have different sampling rates, all channels are resampled to the base rate (highest sampling rate in the file). Resampling uses linear interpolation to fill lower-rate channels.

Apache Arrow IPC

Requires features = ["arrow"].

#![allow(unused)]
fn main() {
use biodream::ArrowOptions;

let df = biodream::read_file("recording.acq")?.into_value();

// Write Arrow IPC stream format
df.to_arrow_ipc("output.arrow", &ArrowOptions::default())?;
}

Arrow IPC files can be read by:

• Python/Polars: pl.read_ipc("output.arrow")
• R: arrow::read_ipc_file("output.arrow")
• Julia: Arrow.Table("output.arrow")

Parquet

Requires features = ["arrow", "parquet"].

#![allow(unused)]
fn main() {
use biodream::ParquetOptions;

let df = biodream::read_file("recording.acq")?.into_value();

df.to_parquet("output.parquet", &ParquetOptions::default())?;
}

Parquet output is compatible with DuckDB, Apache Spark, Pandas, and Polars.

Parquet compression

#![allow(unused)]
fn main() {
use biodream::ParquetOptions;
use parquet::basic::Compression;

let opts = ParquetOptions {
    compression: Compression::SNAPPY,
    ..ParquetOptions::default()
};
df.to_parquet("output.parquet", &opts)?;
}

HDF5

Requires features = ["hdf5"] and the system libhdf5-dev library.

#![allow(unused)]
fn main() {
use biodream::Hdf5Options;

let df = biodream::read_file("recording.acq")?.into_value();

df.to_hdf5("output.h5", &Hdf5Options::default())?;
}

The HDF5 file has the following layout:

/channels/{channel_name}/data   — f64 dataset of scaled samples
/channels/{channel_name}/attrs  — name, units, samples_per_second
/markers/                       — marker dataset with time, label, text
/metadata/                      — revision, recorded_at, byte_order

CLI export

All export formats are also accessible via the biopac convert command. See CLI Reference for full details.