-
Notifications
You must be signed in to change notification settings - Fork 86
/
read.rs
1480 lines (1376 loc) · 54.5 KB
/
read.rs
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
//! 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 },
#[snafu(display(
"Unexpected item header outside a dataset sequence at {:#x}",
bytes_read
))]
UnexpectedItemHeader {
bytes_read: u64,
backtrace: Backtrace,
},
/// Undefined pixel data item length
UndefinedItemLength,
/// Invalid data element length {len:04X} of {tag} at {bytes_read:#x}
InvalidElementLength { tag: Tag, len: u32, bytes_read: u64 },
/// Invalid sequence item length {len:04X} at {bytes_read:#x}
InvalidItemLength { len: u32, bytes_read: u64 },
}
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,
}
/// A strategy for when the parser finds a data element with an odd number
/// in the _length_ header field.
#[derive(Debug, Default, Copy, Clone, Eq, Hash, PartialEq)]
#[non_exhaustive]
pub enum OddLengthStrategy {
/// Accept elements with an odd length as is,
/// continuing data set reading normally.
#[default]
Accept,
/// Assume that the real length is `length + 1`,
/// as in the next even number.
NextEven,
/// Raise an error instead
Fail,
}
/// 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 strategy for handling odd length data elements
pub odd_length: OddLengthStrategy,
/// The position of the reader as received at building time in bytes.
/// Defaults to 0.
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 iterator with the given transfer syntax and options.
#[inline]
pub fn new_with_ts_options(
source: R,
ts: &TransferSyntax,
options: DataSetReaderOptions,
) -> Result<Self>
where
R: Read,
{
Self::new_with_ts_cs_options(source, ts, SpecificCharacterSet::default(), options)
}
/// 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 } => {
let len = match self.sanitize_length(len) {
Some(len) => len,
None => {
return Some(
InvalidItemLengthSnafu {
bytes_read: self.parser.position(),
len: len.0,
}
.fail(),
)
}
};
// entered a new item
self.in_sequence = false;
let last_delimiter = match self.seq_delimiters.last() {
Some(d) => d,
None => {
return Some(
UnexpectedItemHeaderSnafu {
bytes_read: self.parser.position(),
}
.fail(),
)
}
};
self.push_sequence_token(
SeqTokenType::Item,
len,
last_delimiter.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(DecoderError::DecodeItemHeader {
source: dicom_encoding::decode::Error::ReadItemHeader { source, .. },
..
}) if source.kind() == std::io::ErrorKind::UnexpectedEof
&& self.seq_delimiters.pop().is_some_and(|t| t.pixel_data)
=> {
// Note: if `UnexpectedEof` was reached while inside a
// PixelData Sequence, then we assume that
// the end of a DICOM object was reached gracefully.
self.hard_break = true;
None
}
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 } => {
let len = match self.sanitize_length(len) {
Some(len) => len,
None => {
return Some(
InvalidItemLengthSnafu {
bytes_read: self.parser.position(),
len: len.0,
}
.fail(),
)
}
};
// 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,
}) => {
let len = match self.sanitize_length(len) {
Some(len) => len,
None => {
return Some(
InvalidElementLengthSnafu {
tag,
len: len.0,
bytes_read: self.parser.position(),
}
.fail(),
)
}
};
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(mut header) => {
match self.sanitize_length(header.len) {
Some(len) => header.len = len,
None => {
return Some(
InvalidElementLengthSnafu {
tag: header.tag,
len: header.len.0,
bytes_read: self.parser.position(),
}
.fail(),
)
}
};
// 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,
})
}
/// Check for a non-compliant length
/// and handle it according to the current strategy.
/// Returns `None` if the length cannot or should not be resolved.
fn sanitize_length(&self, length: Length) -> Option<Length> {
if length.is_defined() && length.0 & 1 != 0 {
match self.options.odd_length {
OddLengthStrategy::Accept => Some(length),
OddLengthStrategy::NextEven => Some(length + 1),
OddLengthStrategy::Fail => None,
}
} else {
Some(length)
}
}
}
#[cfg(test)]
mod tests {
use super::{DataSetReader, DataToken, StatefulDecode};
use crate::dataset::read::{DataSetReaderOptions, OddLengthStrategy};
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_read_data_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_read_data(data, parser, ground_truth)
}
fn validate_read_data_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_read_data(&data, parser, ground_truth)
}
fn validate_read_data<I, D>(data: &[u8], parser: D, ground_truth: I)
where
I: IntoIterator<Item = DataToken>,
D: StatefulDecode,
{
let dset_reader = DataSetReader::new(parser, Default::default());
validate_data_set_reader(data, dset_reader, ground_truth);
}
fn validate_data_set_reader<S, I>(
data: &[u8],
mut dset_reader: DataSetReader<S>,
ground_truth: I,
) where
S: StatefulDecode,
I: IntoIterator<Item = DataToken>,
{
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_read_data_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_read_data_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_read_data_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_read_data_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