use std::io::{Read, Seek};
use crate::error::{Error, Result};
use crate::filters;
use crate::io::reader::HdfReader;
use super::chunk_read::ChunkReadContext;
use super::{u64_from_usize, usize_from_u64, Dataset, DatasetInfo};
impl Dataset {
pub(super) fn read_chunked_fixed_array<R: Read + Seek>(
reader: &mut HdfReader<R>,
info: &DatasetInfo,
chunk_ctx: &ChunkReadContext<'_>,
) -> Result<Vec<u8>> {
let mut output = Self::scratch_output(chunk_ctx.total_bytes);
Self::read_chunked_fixed_array_into(reader, info, chunk_ctx, &mut output)?;
Ok(output)
}
pub(super) fn read_chunked_fixed_array_into<R: Read + Seek>(
reader: &mut HdfReader<R>,
info: &DatasetInfo,
chunk_ctx: &ChunkReadContext<'_>,
output: &mut [u8],
) -> Result<()> {
if output.len() != chunk_ctx.total_bytes {
return Err(Error::InvalidFormat(format!(
"fixed-array chunk output buffer has {} bytes, expected {}",
output.len(),
chunk_ctx.total_bytes
)));
}
let filtered = info
.filter_pipeline
.as_ref()
.map(|pipeline| !pipeline.filters.is_empty())
.unwrap_or(false);
let chunk_size_len = if filtered {
Self::filtered_chunk_size_len(
info,
chunk_ctx.chunk_bytes,
usize::from(reader.sizeof_size()),
)?
} else {
0
};
let mut elements = Vec::new();
crate::format::fixed_array::read_fixed_array_chunks_into(
reader,
chunk_ctx.idx_addr,
filtered,
chunk_size_len,
&mut elements,
)?;
let chunks_per_dim = Self::chunks_per_dim(chunk_ctx.data_dims, chunk_ctx.chunk_dims)?;
if !Self::has_full_linear_chunk_coverage_1d(elements.iter(), chunk_ctx)? {
Self::filled_data_into(
chunk_ctx.total_bytes / chunk_ctx.element_size,
chunk_ctx.element_size,
info,
output,
)?;
}
let mut compressed_scratch = Vec::new();
let mut raw_scratch = Vec::new();
let mut coords = Vec::with_capacity(chunk_ctx.data_dims.len());
let handled = if Self::linear_index_uses_unfiltered_coalescing(info) {
Self::try_read_coalesced_linear_index_unfiltered_chunks_1d(
reader,
info,
chunk_ctx,
elements.iter(),
"fixed-array chunk size",
output,
)?
} else {
Vec::new()
};
for (chunk_index, element) in elements.iter().enumerate() {
Self::trace_linear_chunk_lookup(
"hdf5.chunk_index.fixed_array.lookup",
chunk_ctx.idx_addr,
u64_from_usize(chunk_index, "fixed-array chunk index")?,
element.addr,
element.nbytes.unwrap_or(u64_from_usize(
chunk_ctx.chunk_bytes,
"fixed-array chunk size",
)?),
element.filter_mask,
);
if crate::io::reader::is_undef_addr(element.addr) {
continue;
}
if handled.get(chunk_index).copied().unwrap_or(false) {
continue;
}
Self::implicit_chunk_coords_into(
chunk_index,
chunk_ctx.chunk_dims,
&chunks_per_dim,
&mut coords,
)?;
let read_size = usize_from_u64(
element.nbytes.unwrap_or(u64_from_usize(
chunk_ctx.chunk_bytes,
"fixed-array chunk size",
)?),
"fixed-array chunk size",
)?;
if Self::try_read_full_chunk_1d_into_output(
reader,
info,
chunk_ctx,
&coords,
element.addr,
read_size,
element.filter_mask,
output,
&mut compressed_scratch,
)? {
continue;
}
Self::read_linear_chunk_payload_into_scratch(
reader,
element.addr,
read_size,
"fixed-array",
chunk_index,
&mut raw_scratch,
)?;
if let Some(ref pipeline) = info.filter_pipeline {
if !pipeline.filters.is_empty() {
let filtered = filters::apply_pipeline_reverse_with_mask_expected(
&raw_scratch,
pipeline,
chunk_ctx.element_size,
element.filter_mask,
chunk_ctx.chunk_bytes,
)?;
Self::copy_chunk_to_output(
&filtered,
&coords,
chunk_ctx.data_dims,
chunk_ctx.chunk_dims,
chunk_ctx.element_size,
output,
)?;
continue;
}
}
Self::copy_chunk_to_output(
&raw_scratch,
&coords,
chunk_ctx.data_dims,
chunk_ctx.chunk_dims,
chunk_ctx.element_size,
output,
)?;
}
Ok(())
}
pub(super) fn read_chunked_extensible_array<R: Read + Seek>(
reader: &mut HdfReader<R>,
info: &DatasetInfo,
chunk_ctx: &ChunkReadContext<'_>,
) -> Result<Vec<u8>> {
let mut output = Self::scratch_output(chunk_ctx.total_bytes);
Self::read_chunked_extensible_array_into(reader, info, chunk_ctx, &mut output)?;
Ok(output)
}
pub(super) fn read_chunked_extensible_array_into<R: Read + Seek>(
reader: &mut HdfReader<R>,
info: &DatasetInfo,
chunk_ctx: &ChunkReadContext<'_>,
output: &mut [u8],
) -> Result<()> {
if output.len() != chunk_ctx.total_bytes {
return Err(Error::InvalidFormat(format!(
"extensible-array chunk output buffer has {} bytes, expected {}",
output.len(),
chunk_ctx.total_bytes
)));
}
let filtered = info
.filter_pipeline
.as_ref()
.map(|pipeline| !pipeline.filters.is_empty())
.unwrap_or(false);
let chunk_size_len = if filtered {
Self::filtered_chunk_size_len(
info,
chunk_ctx.chunk_bytes,
usize::from(reader.sizeof_size()),
)?
} else {
0
};
let mut elements = Vec::new();
crate::format::extensible_array::read_extensible_array_chunks_into(
reader,
chunk_ctx.idx_addr,
filtered,
chunk_size_len,
&mut elements,
)?;
let chunks_per_dim = Self::chunks_per_dim(chunk_ctx.data_dims, chunk_ctx.chunk_dims)?;
if !Self::has_full_linear_chunk_coverage_1d(elements.iter(), chunk_ctx)? {
Self::filled_data_into(
chunk_ctx.total_bytes / chunk_ctx.element_size,
chunk_ctx.element_size,
info,
output,
)?;
}
let mut compressed_scratch = Vec::new();
let mut raw_scratch = Vec::new();
let mut coords = Vec::with_capacity(chunk_ctx.data_dims.len());
let handled = if Self::linear_index_uses_unfiltered_coalescing(info) {
Self::try_read_coalesced_linear_index_unfiltered_chunks_1d(
reader,
info,
chunk_ctx,
elements.iter(),
"extensible-array chunk size",
output,
)?
} else {
Vec::new()
};
for (chunk_index, element) in elements.iter().enumerate() {
Self::trace_linear_chunk_lookup(
"hdf5.chunk_index.extensible_array.lookup",
chunk_ctx.idx_addr,
u64_from_usize(chunk_index, "extensible-array chunk index")?,
element.addr,
element.nbytes.unwrap_or(u64_from_usize(
chunk_ctx.chunk_bytes,
"extensible-array chunk size",
)?),
element.filter_mask,
);
if crate::io::reader::is_undef_addr(element.addr) {
continue;
}
if handled.get(chunk_index).copied().unwrap_or(false) {
continue;
}
Self::implicit_chunk_coords_into(
chunk_index,
chunk_ctx.chunk_dims,
&chunks_per_dim,
&mut coords,
)?;
let read_size = usize_from_u64(
element.nbytes.unwrap_or(u64_from_usize(
chunk_ctx.chunk_bytes,
"extensible-array chunk size",
)?),
"extensible-array chunk size",
)?;
if Self::try_read_full_chunk_1d_into_output(
reader,
info,
chunk_ctx,
&coords,
element.addr,
read_size,
element.filter_mask,
output,
&mut compressed_scratch,
)? {
continue;
}
Self::read_linear_chunk_payload_into_scratch(
reader,
element.addr,
read_size,
"extensible-array",
chunk_index,
&mut raw_scratch,
)?;
if let Some(ref pipeline) = info.filter_pipeline {
if !pipeline.filters.is_empty() {
let filtered = filters::apply_pipeline_reverse_with_mask_expected(
&raw_scratch,
pipeline,
chunk_ctx.element_size,
element.filter_mask,
chunk_ctx.chunk_bytes,
)?;
Self::copy_chunk_to_output(
&filtered,
&coords,
chunk_ctx.data_dims,
chunk_ctx.chunk_dims,
chunk_ctx.element_size,
output,
)?;
continue;
}
}
Self::copy_chunk_to_output(
&raw_scratch,
&coords,
chunk_ctx.data_dims,
chunk_ctx.chunk_dims,
chunk_ctx.element_size,
output,
)?;
}
Ok(())
}
pub(super) fn has_full_linear_chunk_coverage_1d<'a, I>(
elements: I,
chunk_ctx: &ChunkReadContext<'_>,
) -> Result<bool>
where
I: IntoIterator<Item = &'a crate::format::fixed_array::FixedArrayElement>,
{
let Some(expected_chunks) = Self::expected_chunk_count_1d(chunk_ctx)? else {
return Ok(false);
};
let mut count = 0usize;
for element in elements {
if crate::io::reader::is_undef_addr(element.addr) {
return Ok(false);
}
count = count
.checked_add(1)
.ok_or_else(|| Error::InvalidFormat("chunk count overflow".into()))?;
}
Ok(count == expected_chunks)
}
fn linear_index_uses_unfiltered_coalescing(info: &DatasetInfo) -> bool {
info.filter_pipeline
.as_ref()
.map(|pipeline| pipeline.filters.is_empty())
.unwrap_or(true)
}
fn read_linear_chunk_payload_into_scratch<R: Read + Seek>(
reader: &mut HdfReader<R>,
addr: u64,
read_size: usize,
index_name: &'static str,
chunk_index: usize,
scratch: &mut Vec<u8>,
) -> Result<()> {
reader.seek(addr)?;
scratch.resize(read_size, 0);
reader.read_bytes_into(scratch).map_err(|err| {
Error::InvalidFormat(format!(
"failed to read {index_name} chunk {chunk_index} at address {addr} with size {read_size}: {err}"
))
})?;
Ok(())
}
#[cfg(feature = "tracehash")]
fn trace_linear_chunk_lookup(
function: &'static str,
index_addr: u64,
chunk_index: u64,
addr: u64,
nbytes: u64,
filter_mask: u32,
) {
let mut th = tracehash::Call::new(function, file!(), line!());
th.input_u64(index_addr);
th.input_u64(chunk_index);
th.output_value(&(true));
th.output_u64(addr);
th.output_u64(if crate::io::reader::is_undef_addr(addr) {
0
} else {
nbytes
});
th.output_u64(u64::from(filter_mask));
th.finish();
}
#[cfg(not(feature = "tracehash"))]
fn trace_linear_chunk_lookup(
_function: &'static str,
_index_addr: u64,
_chunk_index: u64,
_addr: u64,
_nbytes: u64,
_filter_mask: u32,
) {
}
}