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//! This module contains a mid-level abstraction for reading DICOM content
//! sequentially.
//!
//! The rest of the crate is used to obtain DICOM element headers and values.
//! At this level, headers and values are treated as tokens which can be used
//! to form a syntax tree of a full data set.
use crate::stateful::decode::{DynStatefulDecoder, Error as DecoderError, StatefulDecode};
use dicom_core::header::{DataElementHeader, Header, Length, SequenceItemHeader};
use dicom_core::{PrimitiveValue, Tag, VR};
use dicom_encoding::text::SpecificCharacterSet;
use dicom_encoding::transfer_syntax::TransferSyntax;
use snafu::{Backtrace, ResultExt, Snafu};
use std::cmp::Ordering;
use std::io::Read;
use super::{DataToken, SeqTokenType};
fn is_stateful_decode<T>(_: &T)
where
T: StatefulDecode,
{
}
#[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"))]
ReadItemHeader {
#[snafu(backtrace)]
source: DecoderError,
},
#[snafu(display("Could not read element header"))]
ReadHeader {
#[snafu(backtrace)]
source: DecoderError,
},
#[snafu(display("Could not read {} value bytes for element tagged {}", len, tag))]
ReadValue {
len: u32,
tag: Tag,
#[snafu(backtrace)]
source: DecoderError,
},
#[snafu(display("Could not read {} bytes for item value", len))]
ReadItemValue {
len: u32,
#[snafu(backtrace)]
source: DecoderError,
},
#[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 tag {} while reading element header", tag))]
UnexpectedItemTag { tag: Tag, backtrace: Backtrace },
/// Undefined pixel item length
UndefinedItemLength,
}
pub type Result<T> = std::result::Result<T, Error>;
/// 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,
}
/// The value reading strategy for the data set reader.
///
/// It defines how the `PrimitiveValue`s in value tokens are constructed.
#[derive(Debug, Default, Copy, Clone, Eq, Hash, PartialEq)]
pub enum ValueReadStrategy {
/// Textual values will be decoded according to their value representation.
///
/// Word-sized binary values are read according to
/// the expected byte order.
/// Dates, times, and date-times (DA, DT, TM) are parsed
/// into their more specific variants,
/// leading to parser failure if they are not valid DICOM.
/// String numbers (IS, FD) are also converted into binary representations.
/// For the case of floats, this may introduce precision errors.
Interpreted,
/// Values will be stored without decoding dates or textual numbers.
///
/// Word-sized binary values are read according to
/// the expected byte order.
/// Date-time values and numbers are kept in their original string
/// representation as string objects.
/// All text is still decoded into Rust string values,
/// in accordance to the standard,
/// unless its value representation is unknown to the decoder.
///
/// This is the default strategy.
#[default]
Preserved,
/// All primitive values are fetched as raw byte buffers,
/// without any form of decoding or interpretation.
/// Not even byte order conversions are made.
///
/// This strategy is not recommended,
/// as it makes the retrieval of important textual data more difficult.
Raw,
}
/// The set of options for the data set reader.
#[derive(Debug, Default, Copy, Clone, Eq, Hash, PartialEq)]
#[non_exhaustive]
pub struct DataSetReaderOptions {
/// the value reading strategy
pub value_read: ValueReadStrategy,
/// the position of the reader as received at building time
pub base_offset: u64,
}
impl DataSetReaderOptions {
/// Replace the value reading strategy of the options.
pub fn value_read(mut self, value_read: ValueReadStrategy) -> Self {
self.value_read = value_read;
self
}
/// Replace the base reader offset of the options.
pub fn base_offset(mut self, base_offset: u64) -> Self {
self.base_offset = base_offset;
self
}
}
/// A higher-level reader for retrieving structure in a DICOM data set from an
/// arbitrary data source.
#[derive(Debug)]
pub struct DataSetReader<S> {
/// the stateful decoder
parser: S,
/// the options of this reader
options: DataSetReaderOptions,
/// whether the reader is expecting an item header next (or a sequence delimiter)
in_sequence: bool,
/// whether the reader is expecting the first item value of a pixel sequence next
/// (offset table)
offset_table_next: 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>,
/// if a peek was taken, this holds the token peeked
peek: Option<DataToken>,
}
impl<R> DataSetReader<DynStatefulDecoder<R>> {
/// Create a new data set token reader with the given byte source,
/// while considering the given transfer syntax specifier.
#[inline]
pub fn new_with_ts(source: R, ts: &TransferSyntax) -> Result<Self>
where
R: Read,
{
Self::new_with_ts_cs_options(source, ts, Default::default(), Default::default())
}
/// Create a new data set token reader with the given byte source,
/// while considering the given transfer syntax specifier
/// and the specific character set to assume by default.
///
/// Note that the data set being read
/// can override the character set with the presence of a
/// _Specific Character Set_ data element.
#[inline]
pub fn new_with_ts_cs(source: R, ts: &TransferSyntax, cs: SpecificCharacterSet) -> Result<Self>
where
R: Read,
{
Self::new_with_ts_cs_options(source, ts, cs, Default::default())
}
/// Create a new iterator with the given stateful decoder and options.
pub fn new_with_ts_cs_options(
source: R,
ts: &TransferSyntax,
cs: SpecificCharacterSet,
options: DataSetReaderOptions,
) -> Result<Self>
where
R: Read,
{
let parser = DynStatefulDecoder::new_with(source, ts, cs, 0).context(CreateDecoderSnafu)?;
is_stateful_decode(&parser);
Ok(DataSetReader {
parser,
options,
seq_delimiters: Vec::new(),
delimiter_check_pending: false,
offset_table_next: false,
in_sequence: false,
hard_break: false,
last_header: None,
peek: None,
})
}
}
impl<S> DataSetReader<S> {
/// Create a new iterator with the given stateful decoder and options.
pub fn new(decoder: S, options: DataSetReaderOptions) -> Self {
DataSetReader {
parser: decoder,
options,
seq_delimiters: Vec::new(),
delimiter_check_pending: false,
offset_table_next: false,
in_sequence: false,
hard_break: false,
last_header: None,
peek: None,
}
}
}
impl<S> Iterator for DataSetReader<S>
where
S: StatefulDecode,
{
type Item = Result<DataToken>;
fn next(&mut self) -> Option<Self::Item> {
if self.hard_break {
return None;
}
// if there was a peek, consume peeked token
if let Some(token) = self.peek.take() {
return Some(Ok(token));
}
// 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(DataToken::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(DataToken::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(DataToken::SequenceEnd))
}
}
}
Err(e) => {
self.hard_break = true;
Some(Err(e).context(ReadItemHeaderSnafu))
}
}
} else if let Some(SeqToken {
typ: SeqTokenType::Item,
pixel_data: true,
len,
..
}) = self.seq_delimiters.last()
{
let len = match len.get() {
Some(len) => len as usize,
None => return Some(UndefinedItemLengthSnafu.fail()),
};
if self.offset_table_next {
// offset table
let mut offset_table = Vec::with_capacity(len);
self.offset_table_next = false;
// need to pop item delimiter on the next iteration
self.delimiter_check_pending = true;
Some(
match self.parser.read_u32_to_vec(len as u32, &mut offset_table) {
Ok(()) => Ok(DataToken::OffsetTable(offset_table)),
Err(e) => Err(e).context(ReadItemValueSnafu { len: len as u32 }),
},
)
} else {
// item value
let mut value = Vec::with_capacity(len);
// need to pop item delimiter on the next iteration
self.delimiter_check_pending = true;
Some(
self.parser
.read_to_vec(len as u32, &mut value)
.map(|_| Ok(DataToken::ItemValue(value)))
.unwrap_or_else(|e| Err(e).context(ReadItemValueSnafu { len: len as u32 })),
)
}
} 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;
} else {
self.offset_table_next = true;
}
Some(Ok(DataToken::ItemStart { len }))
}
SequenceItemHeader::SequenceDelimiter => {
// empty pixel data
self.seq_delimiters.pop();
self.in_sequence = false;
Some(Ok(DataToken::SequenceEnd))
}
item => {
self.hard_break = true;
Some(UnexpectedItemTagSnafu { tag: item.tag() }.fail())
}
},
Err(e) => {
self.hard_break = true;
Some(Err(e).context(ReadItemHeaderSnafu))
}
}
} else {
// a plain element header was read, so a value is expected
let value = match self.read_value(&header) {
Ok(v) => v,
Err(e) => {
self.hard_break = true;
self.last_header = None;
return Some(Err(e));
}
};
self.last_header = None;
// sequences can end after this token
self.delimiter_check_pending = true;
Some(Ok(DataToken::PrimitiveValue(value)))
}
} 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(DataToken::SequenceStart { tag, len }))
}
Ok(DataElementHeader {
tag: Tag(0xFFFE, 0xE00D),
..
}) if self.seq_delimiters.is_empty() => {
// ignore delimiter, we are not in a sequence
tracing::warn!(
"Item delimitation item outside of a sequence in position {}",
self.parser.position()
);
// return a new token by calling the method again
self.next()
}
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(DataToken::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(DataToken::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(DataToken::SequenceStart { tag, len }))
}
Ok(header) => {
// save it for the next step
self.last_header = Some(header);
Some(Ok(DataToken::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))
}
}
}
}
}
impl<S> DataSetReader<S>
where
S: StatefulDecode,
{
/// Peek the next token from the source by
/// reading a new token in the first call.
/// Subsequent calls to `peek` will return the same token
/// until another consumer method (such as `Iterator::next`)
/// is called.
pub fn peek(&mut self) -> Result<Option<&DataToken>> {
if self.peek.is_none() {
// try to read the next token
match self.next() {
None => return Ok(None),
Some(Err(e)) => return Err(e),
Some(Ok(token)) => {
self.peek = Some(token);
}
}
}
Ok(self.peek.as_ref())
}
fn update_seq_delimiters(&mut self) -> Result<Option<DataToken>> {
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 = DataToken::SequenceEnd;
}
SeqTokenType::Item => {
self.in_sequence = true;
token = DataToken::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(),
})
}
fn read_value(&mut self, header: &DataElementHeader) -> Result<PrimitiveValue> {
match self.options.value_read {
ValueReadStrategy::Interpreted => self.parser.read_value(header),
ValueReadStrategy::Preserved => self.parser.read_value_preserved(header),
ValueReadStrategy::Raw => self.parser.read_value_bytes(header),
}
.context(ReadValueSnafu {
len: header.len.0,
tag: header.tag,
})
}
}
#[cfg(test)]
mod tests {
use super::{DataSetReader, DataToken, StatefulDecode};
use crate::stateful::decode::StatefulDecoder;
use dicom_core::header::{DataElementHeader, Length};
use dicom_core::value::PrimitiveValue;
use dicom_core::{Tag, VR};
use dicom_encoding::decode::basic::LittleEndianBasicDecoder;
use dicom_encoding::decode::{
explicit_le::ExplicitVRLittleEndianDecoder, implicit_le::ImplicitVRLittleEndianDecoder,
};
use dicom_encoding::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 = DataSetReader::new(parser, Default::default());
let iter = (&mut dset_reader).into_iter();
let mut ground_truth = ground_truth.into_iter();
while let Some(gt_token) = ground_truth.next() {
let token = iter
.next()
.expect("expecting more tokens from reader")
.expect("should fetch the next token without an error");
eprintln!("Next token: {:2?} ; Expected: {:2?}", token, gt_token);
assert_eq!(
token, gt_token,
"Got token {:2?} ; but expected {:2?}",
token, gt_token
);
}
let extra: Vec<_> = iter.collect();
assert_eq!(
extra.len(), // we have already read all of them
0,
"extraneous tokens remaining: {:?}",
extra,
);
assert_eq!(
dset_reader.parser.position(),
data.len() as u64,
"Decoder position did not match end of data",
);
}
#[test]
fn 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 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 read_empty_sequence_explicit() {
static DATA: &[u8] = &[
// SequenceStart: (0008,1032) ProcedureCodeSequence ; len = 0
0x08, 0x00, 0x18, 0x22, // VR: SQ
b'S', b'Q', // Reserved
0x00, 0x00, // Length: 0
0x00, 0x00, 0x00, 0x00,
];
let ground_truth = vec![
DataToken::SequenceStart {
tag: Tag(0x0008, 0x2218),
len: Length(0),
},
DataToken::SequenceEnd,
];
validate_dataset_reader_explicit_vr(DATA, ground_truth);
}
/// Gracefully ignore a stray item end tag in the data set.
#[test]
fn ignore_trailing_item_delimitation_item() {
static DATA: &[u8] = &[
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"
0xfe, 0xff, 0x0d, 0xe0, 0x00, 0x00, 0x00, 0x00, // item end
];
let ground_truth = vec![
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0020, 0x4000),
vr: VR::LT,
len: Length(4),
}),
DataToken::PrimitiveValue(PrimitiveValue::Str("TEST".into())),
// no item end
];
validate_dataset_reader_explicit_vr(DATA, ground_truth);
}
#[test]
fn 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 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 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::OffsetTable(vec![16]),
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 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 peek_data_elements_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, 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::SequenceEnd,
DataToken::ElementHeader(DataElementHeader {
tag: Tag(0x0020, 0x4000),
vr: VR::LT,
len: Length(4),
}),
DataToken::PrimitiveValue(PrimitiveValue::Str("TEST".into())),
];
let mut cursor = DATA;
let parser = StatefulDecoder::new(
&mut cursor,
ExplicitVRLittleEndianDecoder::default(),
LittleEndianBasicDecoder::default(),
SpecificCharacterSet::default(),
);
let mut dset_reader = DataSetReader::new(parser, Default::default());
let iter = (&mut dset_reader).into_iter();
// peek at first token
let token = iter.peek().expect("should peek first token OK");
assert_eq!(token, Some(&ground_truth[0]));
// peeking multiple times gives the same result
let token = iter.peek().expect("should peek first token again OK");
assert_eq!(token, Some(&ground_truth[0]));
// Using `next` give us the same token
let token = iter
.next()
.expect("expected token")
.expect("should read token peeked OK");
assert_eq!(&token, &ground_truth[0]);
// read some more tokens
// sequence end
let token = iter.next().unwrap().unwrap();
assert_eq!(&token, &ground_truth[1]);
// data element header
let token = iter.next().unwrap().unwrap();
assert_eq!(&token, &ground_truth[2]);
// peek string value
let token = iter.peek().unwrap();
assert_eq!(token, Some(&ground_truth[3]));
// peek it again
let token = iter.peek().unwrap();
assert_eq!(token, Some(&ground_truth[3]));
// then read it
let token = iter.next().unwrap().unwrap();
assert_eq!(&token, &ground_truth[3]);
// finished reading, peek should return None
assert!(iter.peek().unwrap().is_none());
}
}