dicom_parser/dataset/lazy_read.rs
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//! This module contains a mid-level abstraction for reading DICOM content
//! sequentially and in a lazy fashion.
//! That is, unlike the reader in the [`read`](super::read) module,
//! DICOM values can be skipped and most allocations can be avoided.
//!
//! At this level, headers and values are treated as tokens which can be used
//! to form a syntax tree of a full data set.
//! Whenever an element value or pixel sequence item is encountered,
//! the given token does not consume the value from the reader,
//! thus letting users decide whether to:
//! - fully read the value and turn it into an in-memory representation;
//! - skip the value altogether, by reading into a sink;
//! - copying the bytes of the value into another writer,
//! such as a previously allocated buffer.
use crate::stateful::decode::{DynStatefulDecoder, Error as DecoderError, StatefulDecode};
use crate::util::ReadSeek;
use dicom_core::header::{DataElementHeader, Header, Length, SequenceItemHeader};
use dicom_core::{Tag, VR};
use dicom_encoding::text::SpecificCharacterSet;
use dicom_encoding::transfer_syntax::TransferSyntax;
use snafu::{Backtrace, OptionExt, ResultExt, Snafu};
use std::cmp::Ordering;
use super::{LazyDataToken, SeqTokenType};
#[derive(Debug, Snafu)]
#[non_exhaustive]
pub enum Error {
#[snafu(display("Could not create decoder"))]
CreateDecoder {
#[snafu(backtrace)]
source: DecoderError,
},
#[snafu(display("Could not read item header at {} bytes", bytes_read))]
ReadItemHeader {
bytes_read: u64,
#[snafu(backtrace)]
source: DecoderError,
},
#[snafu(display("Could not read element header at {} bytes", bytes_read))]
ReadHeader {
bytes_read: u64,
#[snafu(backtrace)]
source: DecoderError,
},
#[snafu(display("Could not read value"))]
ReadValue {
#[snafu(backtrace)]
source: DecoderError,
},
#[snafu(display("Failed to get reader position"))]
GetPosition {
source: std::io::Error,
backtrace: Backtrace,
},
#[snafu(display(
"Inconsistent sequence end: expected end at {} bytes but read {}",
end_of_sequence,
bytes_read
))]
InconsistentSequenceEnd {
end_of_sequence: u64,
bytes_read: u64,
backtrace: Backtrace,
},
#[snafu(display("Unexpected item delimiter at {} bytes", bytes_read))]
UnexpectedItemDelimiter {
bytes_read: u64,
backtrace: Backtrace,
},
#[snafu(display("Unexpected undefined value length at {} bytes", bytes_read))]
UndefinedLength {
bytes_read: u64,
backtrace: Backtrace,
},
}
pub type Result<T, E = Error> = std::result::Result<T, E>;
/// A reader-specific token representing a sequence or item start.
#[derive(Debug, Copy, Clone, PartialEq)]
struct SeqToken {
/// Whether it is the start of a sequence or the start of an item.
typ: SeqTokenType,
/// The length of the value, as indicated by the starting element,
/// can be unknown.
len: Length,
/// Whether this sequence token is part of an encapsulated pixel data.
pixel_data: bool,
/// The number of bytes the parser has read until it reached the
/// beginning of the sequence or item value data.
base_offset: u64,
}
/// An attached iterator for retrieving DICOM object element markers
/// from a random access data source.
///
/// This iterator produces data tokens without eagerly reading the bytes
/// of a value.
#[derive(Debug)]
pub struct LazyDataSetReader<S> {
/// the stateful decoder
parser: S,
/// whether the reader is expecting an item next (or a sequence delimiter)
in_sequence: bool,
/// whether a check for a sequence or item delimitation is pending
delimiter_check_pending: bool,
/// a stack of delimiters
seq_delimiters: Vec<SeqToken>,
/// fuse the iteration process if true
hard_break: bool,
/// last decoded header
last_header: Option<DataElementHeader>,
}
impl<R> LazyDataSetReader<DynStatefulDecoder<R>> {
/// Create a new lazy data set reader
/// with the given random access source and element dictionary,
/// while considering the given transfer syntax and specific character set.
pub fn new_with_ts_cs(
mut source: R,
ts: &TransferSyntax,
cs: SpecificCharacterSet,
) -> Result<Self>
where
R: ReadSeek,
{
let position = source.stream_position().context(GetPositionSnafu)?;
let parser =
DynStatefulDecoder::new_with(source, ts, cs, position).context(CreateDecoderSnafu)?;
Ok(LazyDataSetReader {
parser,
seq_delimiters: Vec::new(),
delimiter_check_pending: false,
in_sequence: false,
hard_break: false,
last_header: None,
})
}
}
impl<S> LazyDataSetReader<S>
where
S: StatefulDecode,
{
/// Create a new iterator with the given stateful decoder.
pub fn new(parser: S) -> Self {
LazyDataSetReader {
parser,
seq_delimiters: Vec::new(),
delimiter_check_pending: false,
in_sequence: false,
hard_break: false,
last_header: None,
}
}
}
impl<S> LazyDataSetReader<S>
where
S: StatefulDecode,
{
fn update_seq_delimiters<'b>(&mut self) -> Result<Option<LazyDataToken<&'b mut S>>> {
if let Some(sd) = self.seq_delimiters.last() {
if let Some(len) = sd.len.get() {
let end_of_sequence = sd.base_offset + len as u64;
let bytes_read = self.parser.position();
match end_of_sequence.cmp(&bytes_read) {
Ordering::Equal => {
// end of delimiter, as indicated by the element's length
let token;
match sd.typ {
SeqTokenType::Sequence => {
self.in_sequence = false;
token = LazyDataToken::SequenceEnd;
}
SeqTokenType::Item => {
self.in_sequence = true;
token = LazyDataToken::ItemEnd;
}
}
self.seq_delimiters.pop();
return Ok(Some(token));
}
Ordering::Less => {
return InconsistentSequenceEndSnafu {
end_of_sequence,
bytes_read,
}
.fail();
}
Ordering::Greater => {} // continue normally
}
}
}
self.delimiter_check_pending = false;
Ok(None)
}
#[inline]
fn push_sequence_token(&mut self, typ: SeqTokenType, len: Length, pixel_data: bool) {
self.seq_delimiters.push(SeqToken {
typ,
pixel_data,
len,
base_offset: self.parser.position(),
})
}
/// Retrieve the inner stateful decoder from this data set reader.
pub fn into_decoder(self) -> S {
self.parser
}
/// Advance and retrieve the next DICOM data token.
///
/// **Note:** For the data set to be successfully parsed,
/// the resulting data tokens needs to be consumed
/// if they are of a value type.
pub fn advance(&mut self) -> Option<Result<LazyDataToken<&mut S>>> {
if self.hard_break {
return None;
}
// record the reading position before any further reading
let bytes_read = self.parser.position();
// item or sequence delimitation logic for explicit lengths
if self.delimiter_check_pending {
match self.update_seq_delimiters() {
Err(e) => {
self.hard_break = true;
return Some(Err(e));
}
Ok(Some(token)) => return Some(Ok(token)),
Ok(None) => { /* no-op */ }
}
}
if self.in_sequence {
// at sequence level, expecting item header
match self.parser.decode_item_header() {
Ok(header) => {
match header {
SequenceItemHeader::Item { len } => {
// entered a new item
self.in_sequence = false;
self.push_sequence_token(
SeqTokenType::Item,
len,
self.seq_delimiters.last()
.expect("item header should be read only inside an existing sequence")
.pixel_data);
// items can be empty
if len == Length(0) {
self.delimiter_check_pending = true;
}
Some(Ok(LazyDataToken::ItemStart { len }))
}
SequenceItemHeader::ItemDelimiter => {
// closed an item
self.seq_delimiters.pop();
self.in_sequence = true;
// sequences can end after an item delimiter
self.delimiter_check_pending = true;
Some(Ok(LazyDataToken::ItemEnd))
}
SequenceItemHeader::SequenceDelimiter => {
// closed a sequence
self.seq_delimiters.pop();
self.in_sequence = false;
// items can end after a nested sequence ends
self.delimiter_check_pending = true;
Some(Ok(LazyDataToken::SequenceEnd))
}
}
}
Err(e) => {
self.hard_break = true;
Some(Err(e).context(ReadItemHeaderSnafu { bytes_read }))
}
}
} else if let Some(SeqToken {
typ: SeqTokenType::Item,
pixel_data: true,
len,
..
}) = self.seq_delimiters.last()
{
// item value
let len = match len
.get()
.with_context(|| UndefinedLengthSnafu { bytes_read })
{
Ok(len) => len,
Err(e) => return Some(Err(e)),
};
// need to pop item delimiter on the next iteration
self.delimiter_check_pending = true;
Some(Ok(LazyDataToken::LazyItemValue {
len,
decoder: &mut self.parser,
}))
} else if let Some(header) = self.last_header {
if header.is_encapsulated_pixeldata() {
self.push_sequence_token(SeqTokenType::Sequence, Length::UNDEFINED, true);
self.last_header = None;
// encapsulated pixel data, expecting offset table
match self.parser.decode_item_header() {
Ok(header) => match header {
SequenceItemHeader::Item { len } => {
// entered a new item
self.in_sequence = false;
self.push_sequence_token(SeqTokenType::Item, len, true);
// items can be empty
if len == Length(0) {
self.delimiter_check_pending = true;
}
Some(Ok(LazyDataToken::ItemStart { len }))
}
SequenceItemHeader::SequenceDelimiter => {
// empty pixel data
self.seq_delimiters.pop();
self.in_sequence = false;
Some(Ok(LazyDataToken::SequenceEnd))
}
SequenceItemHeader::ItemDelimiter => {
self.hard_break = true;
Some(UnexpectedItemDelimiterSnafu { bytes_read }.fail())
}
},
Err(e) => {
self.hard_break = true;
Some(Err(e).context(ReadItemHeaderSnafu { bytes_read }))
}
}
} else {
// a plain element header was read, so an element value is expected
self.last_header = None;
// sequences can end after this token
self.delimiter_check_pending = true;
Some(Ok(LazyDataToken::LazyValue {
header,
decoder: &mut self.parser,
}))
}
} else {
// a data element header or item delimiter is expected
match self.parser.decode_header() {
Ok(DataElementHeader {
tag,
vr: VR::SQ,
len,
}) => {
self.in_sequence = true;
self.push_sequence_token(SeqTokenType::Sequence, len, false);
// sequences can end right after they start
if len == Length(0) {
self.delimiter_check_pending = true;
}
Some(Ok(LazyDataToken::SequenceStart { tag, len }))
}
Ok(DataElementHeader {
tag: Tag(0xFFFE, 0xE00D),
..
}) => {
self.in_sequence = true;
// pop item delimiter
self.seq_delimiters.pop();
// sequences can end after this token
self.delimiter_check_pending = true;
Some(Ok(LazyDataToken::ItemEnd))
}
Ok(header) if header.is_encapsulated_pixeldata() => {
// encapsulated pixel data conditions:
// expect a sequence of pixel data fragments
// save it for the next step
self.last_header = Some(header);
Some(Ok(LazyDataToken::PixelSequenceStart))
}
Ok(header) if header.len.is_undefined() => {
// treat other undefined length elements
// as data set sequences,
// discarding the VR in the process
self.in_sequence = true;
let DataElementHeader { tag, len, .. } = header;
self.push_sequence_token(SeqTokenType::Sequence, len, false);
Some(Ok(LazyDataToken::SequenceStart { tag, len }))
}
Ok(header) => {
// save it for the next step
self.last_header = Some(header);
Some(Ok(LazyDataToken::ElementHeader(header)))
}
Err(DecoderError::DecodeElementHeader {
source: dicom_encoding::decode::Error::ReadHeaderTag { source, .. },
..
}) if source.kind() == std::io::ErrorKind::UnexpectedEof => {
// Note: if `UnexpectedEof` was reached while trying to read
// an element tag, then we assume that
// the end of a DICOM object was reached gracefully.
// This approach is unlikely to consume trailing bytes,
// but may ignore the current depth of the data set tree.
self.hard_break = true;
None
}
Err(e) => {
self.hard_break = true;
Some(Err(e).context(ReadHeaderSnafu { bytes_read }))
}
}
}
}
}
#[cfg(test)]
mod tests {
use super::{LazyDataSetReader, StatefulDecode};
use crate::{
dataset::{DataToken, LazyDataToken},
StatefulDecoder,
};
use dicom_core::value::PrimitiveValue;
use dicom_core::{
dicom_value,
header::{DataElementHeader, Length},
};
use dicom_core::{Tag, VR};
use dicom_encoding::decode::{
explicit_le::ExplicitVRLittleEndianDecoder, implicit_le::ImplicitVRLittleEndianDecoder,
};
use dicom_encoding::{decode::basic::LittleEndianBasicDecoder, text::SpecificCharacterSet};
fn validate_dataset_reader_implicit_vr<I>(data: &[u8], ground_truth: I)
where
I: IntoIterator<Item = DataToken>,
{
let mut cursor = data;
let parser = StatefulDecoder::new(
&mut cursor,
ImplicitVRLittleEndianDecoder::default(),
LittleEndianBasicDecoder::default(),
SpecificCharacterSet::default(),
);
validate_dataset_reader(data, parser, ground_truth)
}
fn validate_dataset_reader_explicit_vr<I>(data: &[u8], ground_truth: I)
where
I: IntoIterator<Item = DataToken>,
{
let mut cursor = data;
let parser = StatefulDecoder::new(
&mut cursor,
ExplicitVRLittleEndianDecoder::default(),
LittleEndianBasicDecoder::default(),
SpecificCharacterSet::default(),
);
validate_dataset_reader(&data, parser, ground_truth)
}
fn validate_dataset_reader<I, D>(data: &[u8], parser: D, ground_truth: I)
where
I: IntoIterator<Item = DataToken>,
D: StatefulDecode,
{
let mut dset_reader = LazyDataSetReader::new(parser);
let mut gt_iter = ground_truth.into_iter();
while let Some(res) = dset_reader.advance() {
let gt_token = gt_iter.next().expect("ground truth is shorter");
let token = res.expect("should parse without an error");
let token = token.into_owned().unwrap();
assert_eq!(token, gt_token);
}
assert_eq!(
gt_iter.count(), // consume til the end
0, // we have already read all of them
"unexpected number of tokens remaining"
);
assert_eq!(dset_reader.parser.position(), data.len() as u64);
}
#[test]
fn lazy_read_sequence_explicit() {
#[rustfmt::skip]
static DATA: &[u8] = &[
0x18, 0x00, 0x11, 0x60, // sequence tag: (0018,6011) SequenceOfUltrasoundRegions
b'S', b'Q', // VR
0x00, 0x00, // reserved
0x2e, 0x00, 0x00, 0x00, // length: 28 + 18 = 46 (#= 2)
// -- 12 --
0xfe, 0xff, 0x00, 0xe0, // item start tag
0x14, 0x00, 0x00, 0x00, // item length: 20 (#= 2)
// -- 20 --
0x18, 0x00, 0x12, 0x60, b'U', b'S', 0x02, 0x00, 0x01, 0x00, // (0018, 6012) RegionSpatialformat, len = 2, value = 1
// -- 30 --
0x18, 0x00, 0x14, 0x60, b'U', b'S', 0x02, 0x00, 0x02, 0x00, // (0018, 6012) RegionDataType, len = 2, value = 2
// -- 40 --
0xfe, 0xff, 0x00, 0xe0, // item start tag
0x0a, 0x00, 0x00, 0x00, // item length: 10 (#= 1)
// -- 48 --
0x18, 0x00, 0x12, 0x60, b'U', b'S', 0x02, 0x00, 0x04, 0x00, // (0018, 6012) RegionSpatialformat, len = 2, value = 4
// -- 58 --
0x20, 0x00, 0x00, 0x40, b'L', b'T', 0x04, 0x00, // (0020,4000) ImageComments, len = 4
b'T', b'E', b'S', b'T', // value = "TEST"
];
let ground_truth = vec![
DataToken::SequenceStart {
tag: Tag(0x0018, 0x6011),
len: Length(46),
},
DataToken::ItemStart { len: Length(20) },
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0018, 0x6012),
vr: VR::US,
len: Length(2),
}),
DataToken::PrimitiveValue(PrimitiveValue::U16([1].as_ref().into())),
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0018, 0x6014),
vr: VR::US,
len: Length(2),
}),
DataToken::PrimitiveValue(PrimitiveValue::U16([2].as_ref().into())),
DataToken::ItemEnd,
DataToken::ItemStart { len: Length(10) },
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0018, 0x6012),
vr: VR::US,
len: Length(2),
}),
DataToken::PrimitiveValue(PrimitiveValue::U16([4].as_ref().into())),
DataToken::ItemEnd,
DataToken::SequenceEnd,
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0020, 0x4000),
vr: VR::LT,
len: Length(4),
}),
DataToken::PrimitiveValue(PrimitiveValue::Str("TEST".into())),
];
validate_dataset_reader_explicit_vr(DATA, ground_truth);
}
#[test]
fn lazy_read_sequence_explicit_2() {
static DATA: &[u8] = &[
// SequenceStart: (0008,2218) ; len = 54 (#=3)
0x08, 0x00, 0x18, 0x22, b'S', b'Q', 0x00, 0x00, 0x36, 0x00, 0x00, 0x00,
// -- 12, --
// ItemStart: len = 46
0xfe, 0xff, 0x00, 0xe0, 0x2e, 0x00, 0x00, 0x00,
// -- 20, --
// ElementHeader: (0008,0100) CodeValue; len = 8
0x08, 0x00, 0x00, 0x01, b'S', b'H', 0x08, 0x00, // PrimitiveValue
0x54, 0x2d, 0x44, 0x31, 0x32, 0x31, 0x33, b' ',
// -- 36, --
// ElementHeader: (0008,0102) CodingSchemeDesignator; len = 4
0x08, 0x00, 0x02, 0x01, b'S', b'H', 0x04, 0x00, // PrimitiveValue
0x53, 0x52, 0x54, b' ',
// -- 48, --
// (0008,0104) CodeMeaning; len = 10
0x08, 0x00, 0x04, 0x01, b'L', b'O', 0x0a, 0x00, // PrimitiveValue
0x4a, 0x61, 0x77, b' ', 0x72, 0x65, 0x67, 0x69, 0x6f, 0x6e,
// -- 66 --
// SequenceStart: (0040,0555) AcquisitionContextSequence; len = 0
0x40, 0x00, 0x55, 0x05, b'S', b'Q', 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
// ElementHeader: (2050,0020) PresentationLUTShape; len = 8
0x50, 0x20, 0x20, 0x00, b'C', b'S', 0x08, 0x00, // PrimitiveValue
b'I', b'D', b'E', b'N', b'T', b'I', b'T', b'Y',
];
let ground_truth = vec![
DataToken::SequenceStart {
tag: Tag(0x0008, 0x2218),
len: Length(54),
},
DataToken::ItemStart { len: Length(46) },
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0008, 0x0100),
vr: VR::SH,
len: Length(8),
}),
DataToken::PrimitiveValue(PrimitiveValue::Strs(
["T-D1213 ".to_owned()].as_ref().into(),
)),
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0008, 0x0102),
vr: VR::SH,
len: Length(4),
}),
DataToken::PrimitiveValue(PrimitiveValue::Strs(["SRT ".to_owned()].as_ref().into())),
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0008, 0x0104),
vr: VR::LO,
len: Length(10),
}),
DataToken::PrimitiveValue(PrimitiveValue::Strs(
["Jaw region".to_owned()].as_ref().into(),
)),
DataToken::ItemEnd,
DataToken::SequenceEnd,
DataToken::SequenceStart {
tag: Tag(0x0040, 0x0555),
len: Length(0),
},
DataToken::SequenceEnd,
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x2050, 0x0020),
vr: VR::CS,
len: Length(8),
}),
DataToken::PrimitiveValue(PrimitiveValue::Strs(
["IDENTITY".to_owned()].as_ref().into(),
)),
];
validate_dataset_reader_explicit_vr(DATA, ground_truth);
}
#[test]
fn lazy_read_sequence_implicit() {
#[rustfmt::skip]
static DATA: &[u8] = &[
0x18, 0x00, 0x11, 0x60, // sequence tag: (0018,6011) SequenceOfUltrasoundRegions
b'S', b'Q', // VR
0x00, 0x00, // reserved
0xff, 0xff, 0xff, 0xff, // length: undefined
// -- 12 --
0xfe, 0xff, 0x00, 0xe0, // item start tag
0xff, 0xff, 0xff, 0xff, // item length: undefined
// -- 20 --
0x18, 0x00, 0x12, 0x60, b'U', b'S', 0x02, 0x00, 0x01, 0x00, // (0018, 6012) RegionSpatialformat, len = 2, value = 1
// -- 30 --
0x18, 0x00, 0x14, 0x60, b'U', b'S', 0x02, 0x00, 0x02, 0x00, // (0018, 6012) RegionDataType, len = 2, value = 2
// -- 40 --
0xfe, 0xff, 0x0d, 0xe0, 0x00, 0x00, 0x00, 0x00, // item end
// -- 48 --
0xfe, 0xff, 0x00, 0xe0, // item start tag
0xff, 0xff, 0xff, 0xff, // item length: undefined
// -- 56 --
0x18, 0x00, 0x12, 0x60, b'U', b'S', 0x02, 0x00, 0x04, 0x00, // (0018, 6012) RegionSpatialformat, len = 2, value = 4
// -- 66 --
0xfe, 0xff, 0x0d, 0xe0, 0x00, 0x00, 0x00, 0x00, // item end
// -- 74 --
0xfe, 0xff, 0xdd, 0xe0, 0x00, 0x00, 0x00, 0x00, // sequence end
// -- 82 --
0x20, 0x00, 0x00, 0x40, b'L', b'T', 0x04, 0x00, // (0020,4000) ImageComments, len = 4
b'T', b'E', b'S', b'T', // value = "TEST"
];
let ground_truth = vec![
DataToken::SequenceStart {
tag: Tag(0x0018, 0x6011),
len: Length::UNDEFINED,
},
DataToken::ItemStart {
len: Length::UNDEFINED,
},
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0018, 0x6012),
vr: VR::US,
len: Length(2),
}),
DataToken::PrimitiveValue(PrimitiveValue::U16([1].as_ref().into())),
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0018, 0x6014),
vr: VR::US,
len: Length(2),
}),
DataToken::PrimitiveValue(PrimitiveValue::U16([2].as_ref().into())),
DataToken::ItemEnd,
DataToken::ItemStart {
len: Length::UNDEFINED,
},
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0018, 0x6012),
vr: VR::US,
len: Length(2),
}),
DataToken::PrimitiveValue(PrimitiveValue::U16([4].as_ref().into())),
DataToken::ItemEnd,
DataToken::SequenceEnd,
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0020, 0x4000),
vr: VR::LT,
len: Length(4),
}),
DataToken::PrimitiveValue(PrimitiveValue::Str("TEST".into())),
];
validate_dataset_reader_explicit_vr(DATA, ground_truth);
}
#[test]
fn lazy_read_dataset_in_dataset() {
#[rustfmt::skip]
const DATA: &'static [u8; 138] = &[
// 0: (2001, 9000) private sequence
0x01, 0x20, 0x00, 0x90, //
// length: undefined
0xFF, 0xFF, 0xFF, 0xFF, //
// 8: Item start
0xFE, 0xFF, 0x00, 0xE0, //
// Item length explicit (114 bytes)
0x72, 0x00, 0x00, 0x00, //
// 16: (0008,1115) ReferencedSeriesSequence
0x08, 0x00, 0x15, 0x11, //
// length: undefined
0xFF, 0xFF, 0xFF, 0xFF, //
// 24: Item start
0xFE, 0xFF, 0x00, 0xE0, //
// Item length undefined
0xFF, 0xFF, 0xFF, 0xFF, //
// 32: (0008,1140) ReferencedImageSequence
0x08, 0x00, 0x40, 0x11, //
// length: undefined
0xFF, 0xFF, 0xFF, 0xFF, //
// 40: Item start
0xFE, 0xFF, 0x00, 0xE0, //
// Item length undefined
0xFF, 0xFF, 0xFF, 0xFF, //
// 48: (0008,1150) ReferencedSOPClassUID
0x08, 0x00, 0x50, 0x11, //
// length: 26
0x1a, 0x00, 0x00, 0x00, //
// Value: "1.2.840.10008.5.1.4.1.1.7\0" (SecondaryCaptureImageStorage)
b'1', b'.', b'2', b'.', b'8', b'4', b'0', b'.', b'1', b'0', b'0', b'0', b'8', b'.',
b'5', b'.', b'1', b'.', b'4', b'.', b'1', b'.', b'1', b'.', b'7', b'\0',
// 82: Item End (ReferencedImageSequence)
0xFE, 0xFF, 0x0D, 0xE0, //
0x00, 0x00, 0x00, 0x00, //
// 90: Sequence End (ReferencedImageSequence)
0xFE, 0xFF, 0xDD, 0xE0, //
0x00, 0x00, 0x00, 0x00, //
// 98: Item End (ReferencedSeriesSequence)
0xFE, 0xFF, 0x0D, 0xE0, //
0x00, 0x00, 0x00, 0x00, //
// 106: Sequence End (ReferencedSeriesSequence)
0xFE, 0xFF, 0xDD, 0xE0, //
0x00, 0x00, 0x00, 0x00, //
// 114: (2050,0020) PresentationLUTShape (CS)
0x50, 0x20, 0x20, 0x00, //
// length: 8
0x08, 0x00, 0x00, 0x00, //
b'I', b'D', b'E', b'N', b'T', b'I', b'T', b'Y', //
// 130: Sequence end
0xFE, 0xFF, 0xDD, 0xE0, //
0x00, 0x00, 0x00, 0x00, //
];
let ground_truth = vec![
DataToken::SequenceStart {
tag: Tag(0x2001, 0x9000),
len: Length::UNDEFINED,
},
DataToken::ItemStart { len: Length(114) },
DataToken::SequenceStart {
tag: Tag(0x0008, 0x1115),
len: Length::UNDEFINED,
},
DataToken::ItemStart {
len: Length::UNDEFINED,
},
DataToken::SequenceStart {
tag: Tag(0x0008, 0x1140),
len: Length::UNDEFINED,
},
DataToken::ItemStart {
len: Length::UNDEFINED,
},
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0008, 0x1150),
vr: VR::UI,
len: Length(26),
}),
DataToken::PrimitiveValue(PrimitiveValue::from("1.2.840.10008.5.1.4.1.1.7\0")),
DataToken::ItemEnd,
DataToken::SequenceEnd,
DataToken::ItemEnd,
DataToken::SequenceEnd,
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x2050, 0x0020),
vr: VR::CS,
len: Length(8),
}),
DataToken::PrimitiveValue(PrimitiveValue::from("IDENTITY")),
DataToken::ItemEnd, // inserted automatically
DataToken::SequenceEnd,
];
validate_dataset_reader_implicit_vr(DATA, ground_truth);
}
#[test]
fn lazy_read_implicit_len_sequence_implicit_vr_unknown() {
#[rustfmt::skip]
static DATA: &[u8] = &[
0x33, 0x55, 0x33, 0x55, // sequence tag: (5533,5533) «private, unknown attribute»
0xff, 0xff, 0xff, 0xff, // length: undefined
// -- 8 --
0xfe, 0xff, 0x00, 0xe0, // item begin
0xff, 0xff, 0xff, 0xff, // length: undefined
// -- 16 --
0xfe, 0xff, 0x0d, 0xe0, // item end
0x00, 0x00, 0x00, 0x00, // length is always zero
// -- 24 --
0xfe, 0xff, 0xdd, 0xe0,
0x00, 0x00, 0x00, 0x00, // sequence end
// -- 32 --
];
let ground_truth = vec![
DataToken::SequenceStart {
tag: Tag(0x5533, 0x5533),
len: Length::UNDEFINED,
},
DataToken::ItemStart {
len: Length::UNDEFINED,
},
DataToken::ItemEnd,
DataToken::SequenceEnd,
];
validate_dataset_reader_implicit_vr(DATA, ground_truth);
}
#[test]
fn read_encapsulated_pixeldata() {
#[rustfmt::skip]
static DATA: &[u8] = &[
0xe0, 0x7f, 0x10, 0x00, // (7FE0, 0010) PixelData
b'O', b'B', // VR
0x00, 0x00, // reserved
0xff, 0xff, 0xff, 0xff, // length: undefined
// -- 12 -- Basic offset table
0xfe, 0xff, 0x00, 0xe0, // item start tag
0x00, 0x00, 0x00, 0x00, // item length: 0
// -- 20 -- First fragment of pixel data
0xfe, 0xff, 0x00, 0xe0, // item start tag
0x20, 0x00, 0x00, 0x00, // item length: 32
// -- 28 -- Compressed Fragment
0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99,
0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99,
0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99,
0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99,
// -- 60 -- End of pixel data
0xfe, 0xff, 0xdd, 0xe0, // sequence end tag
0x00, 0x00, 0x00, 0x00,
// -- 68 -- padding
0xfc, 0xff, 0xfc, 0xff, // (fffc,fffc) DataSetTrailingPadding
b'O', b'B', // VR
0x00, 0x00, // reserved
0x08, 0x00, 0x00, 0x00, // length: 8
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
];
let ground_truth = vec![
DataToken::PixelSequenceStart,
DataToken::ItemStart { len: Length(0) },
DataToken::ItemEnd,
DataToken::ItemStart { len: Length(32) },
DataToken::ItemValue(vec![0x99; 32]),
DataToken::ItemEnd,
DataToken::SequenceEnd,
DataToken::ElementHeader(DataElementHeader::new(
Tag(0xfffc, 0xfffc),
VR::OB,
Length(8),
)),
DataToken::PrimitiveValue(PrimitiveValue::U8([0x00; 8].as_ref().into())),
];
validate_dataset_reader_explicit_vr(DATA, ground_truth);
}
#[test]
fn lazy_read_encapsulated_pixeldata_with_offset_table() {
#[rustfmt::skip]
static DATA: &[u8] = &[
0xe0, 0x7f, 0x10, 0x00, // (7FE0, 0010) PixelData
b'O', b'B', // VR
0x00, 0x00, // reserved
0xff, 0xff, 0xff, 0xff, // length: undefined
// -- 12 -- Basic offset table
0xfe, 0xff, 0x00, 0xe0, // item start tag
0x04, 0x00, 0x00, 0x00, // item length: 4
// -- 20 -- item value
0x10, 0x00, 0x00, 0x00, // 16
// -- 24 -- First fragment of pixel data
0xfe, 0xff, 0x00, 0xe0, // item start tag
0x20, 0x00, 0x00, 0x00, // item length: 32
// -- 32 -- Compressed Fragment
0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99,
0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99,
0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99,
0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99, 0x99,
// -- 60 -- End of pixel data
0xfe, 0xff, 0xdd, 0xe0, // sequence end tag
0x00, 0x00, 0x00, 0x00,
// -- 68 -- padding
0xfc, 0xff, 0xfc, 0xff, // (fffc,fffc) DataSetTrailingPadding
b'O', b'B', // VR
0x00, 0x00, // reserved
0x08, 0x00, 0x00, 0x00, // length: 8
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
];
let ground_truth = vec![
DataToken::PixelSequenceStart,
DataToken::ItemStart { len: Length(4) },
DataToken::ItemValue(vec![0x10, 0x00, 0x00, 0x00]),
DataToken::ItemEnd,
DataToken::ItemStart { len: Length(32) },
DataToken::ItemValue(vec![0x99; 32]),
DataToken::ItemEnd,
DataToken::SequenceEnd,
DataToken::ElementHeader(DataElementHeader::new(
Tag(0xfffc, 0xfffc),
VR::OB,
Length(8),
)),
DataToken::PrimitiveValue(PrimitiveValue::U8([0x00; 8].as_ref().into())),
];
validate_dataset_reader_explicit_vr(DATA, ground_truth);
}
#[test]
fn lazy_read_sequence_explicit_2_skip_values() {
static DATA: &[u8] = &[
// SequenceStart: (0008,2218) ; len = 54 (#=3)
0x08, 0x00, 0x18, 0x22, b'S', b'Q', 0x00, 0x00, 0x36, 0x00, 0x00, 0x00,
// -- 12, --
// ItemStart: len = 46
0xfe, 0xff, 0x00, 0xe0, 0x2e, 0x00, 0x00, 0x00,
// -- 20, --
// ElementHeader: (0008,0100) CodeValue; len = 8
0x08, 0x00, 0x00, 0x01, b'S', b'H', 0x08, 0x00, // PrimitiveValue
0x54, 0x2d, 0x44, 0x31, 0x32, 0x31, 0x33, b' ',
// -- 36, --
// ElementHeader: (0008,0102) CodingSchemeDesignator; len = 4
0x08, 0x00, 0x02, 0x01, b'S', b'H', 0x04, 0x00, // PrimitiveValue
0x53, 0x52, 0x54, b' ',
// -- 48, --
// (0008,0104) CodeMeaning; len = 10
0x08, 0x00, 0x04, 0x01, b'L', b'O', 0x0a, 0x00, // PrimitiveValue
0x4a, 0x61, 0x77, b' ', 0x72, 0x65, 0x67, 0x69, 0x6f, 0x6e,
// -- 66 --
// SequenceStart: (0040,0555) AcquisitionContextSequence; len = 0
0x40, 0x00, 0x55, 0x05, b'S', b'Q', 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
// ElementHeader: (2050,0020) PresentationLUTShape; len = 8
0x50, 0x20, 0x20, 0x00, b'C', b'S', 0x08, 0x00, // PrimitiveValue
b'I', b'D', b'E', b'N', b'T', b'I', b'T', b'Y',
];
let ground_truth = vec![
DataToken::SequenceStart {
tag: Tag(0x0008, 0x2218),
len: Length(54),
},
DataToken::ItemStart { len: Length(46) },
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0008, 0x0100),
vr: VR::SH,
len: Length(8),
}),
DataToken::PrimitiveValue(PrimitiveValue::Strs(
["T-D1213 ".to_owned()].as_ref().into(),
)),
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0008, 0x0102),
vr: VR::SH,
len: Length(4),
}),
DataToken::PrimitiveValue(PrimitiveValue::Strs(["SRT ".to_owned()].as_ref().into())),
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0008, 0x0104),
vr: VR::LO,
len: Length(10),
}),
DataToken::PrimitiveValue(PrimitiveValue::Strs(
["Jaw region".to_owned()].as_ref().into(),
)),
DataToken::ItemEnd,
DataToken::SequenceEnd,
DataToken::SequenceStart {
tag: Tag(0x0040, 0x0555),
len: Length(0),
},
DataToken::SequenceEnd,
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x2050, 0x0020),
vr: VR::CS,
len: Length(8),
}),
DataToken::PrimitiveValue(PrimitiveValue::Strs(
["IDENTITY".to_owned()].as_ref().into(),
)),
];
let mut cursor = DATA;
let parser = StatefulDecoder::new(
&mut cursor,
ExplicitVRLittleEndianDecoder::default(),
LittleEndianBasicDecoder::default(),
SpecificCharacterSet::default(),
);
let mut dset_reader = LazyDataSetReader::new(parser);
let mut gt_iter = ground_truth.into_iter();
while let Some(res) = dset_reader.advance() {
let token = res.expect("should parse without an error");
let gt_token = gt_iter.next().expect("ground truth is shorter");
match token {
LazyDataToken::LazyValue { .. } | LazyDataToken::LazyItemValue { .. } => {
token.skip().unwrap();
}
token => {
let token = token.into_owned().unwrap();
assert_eq!(token, gt_token);
}
}
}
assert_eq!(
gt_iter.count(), // consume til the end
0, // we have already read all of them
"unexpected number of tokens remaining"
);
assert_eq!(dset_reader.parser.position(), DATA.len() as u64);
}
#[test]
fn lazy_read_value_via_into_value() {
// manually crafted DICOM data elements
// Tag: (0002,0002) Media Storage SOP Class UID
// VR: UI
// Length: 26
// Value: "1.2.840.10008.5.1.4.1.1.1\0"
// --
// Tag: (0002,0010) Transfer Syntax UID
// VR: UI
// Length: 20
// Value: "1.2.840.10008.1.2.1\0" == ExplicitVRLittleEndian
// --
const RAW: &'static [u8; 62] = &[
0x02, 0x00, 0x02, 0x00, 0x55, 0x49, 0x1a, 0x00, 0x31, 0x2e, 0x32, 0x2e, 0x38, 0x34,
0x30, 0x2e, 0x31, 0x30, 0x30, 0x30, 0x38, 0x2e, 0x35, 0x2e, 0x31, 0x2e, 0x34, 0x2e,
0x31, 0x2e, 0x31, 0x2e, 0x31, 0x00, 0x02, 0x00, 0x10, 0x00, 0x55, 0x49, 0x14, 0x00,
0x31, 0x2e, 0x32, 0x2e, 0x38, 0x34, 0x30, 0x2e, 0x31, 0x30, 0x30, 0x30, 0x38, 0x2e,
0x31, 0x2e, 0x32, 0x2e, 0x31, 0x00,
];
let mut cursor = &RAW[..];
let parser = StatefulDecoder::new(
&mut cursor,
ExplicitVRLittleEndianDecoder::default(),
LittleEndianBasicDecoder::default(),
SpecificCharacterSet::default(),
);
let mut dset_reader = LazyDataSetReader::new(parser);
let token = dset_reader
.advance()
.expect("Expected token 1")
.expect("Failed to read token 1");
let header_token1 = match token {
LazyDataToken::ElementHeader(header) => header,
_ => {
panic!("Unexpected token type (1)");
}
};
let token = dset_reader
.advance()
.expect("Expected token 2")
.expect("Failed to read token 2");
match token {
LazyDataToken::LazyValue { header, decoder: _ } => {
assert_eq!(header_token1, header);
}
_ => {
panic!("Unexpected token type (2)");
}
}
// consume via into_value
assert_eq!(
token.into_value().unwrap(),
dicom_value!(Strs, ["1.2.840.10008.5.1.4.1.1.1\0"]),
);
let token = dset_reader
.advance()
.expect("Expected token 3")
.expect("Failed to read token 3");
let header_token3 = match token {
LazyDataToken::ElementHeader(header) => header,
_ => {
panic!("Unexpected token type (3)");
}
};
let token = dset_reader
.advance()
.expect("Expected token 4")
.expect("Failed to read token 4");
match token {
LazyDataToken::LazyValue { header, decoder: _ } => {
assert_eq!(header_token3, header);
}
_ => {
panic!("Unexpected token type (4)");
}
}
// consume via into_value
assert_eq!(
token.into_value().unwrap(),
dicom_value!(Strs, ["1.2.840.10008.1.2.1\0"]),
);
assert!(
dset_reader.advance().is_none(),
"unexpected number of tokens remaining"
);
}
}