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DicomFlowsTest.scala
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DicomFlowsTest.scala
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package com.exini.dicom.streams
import akka.actor.ActorSystem
import akka.stream.scaladsl.{ FileIO, Sink, Source }
import akka.stream.testkit.scaladsl.TestSink
import akka.testkit.TestKit
import akka.util.ByteString
import com.exini.dicom.data.DicomElements.ValueElement
import com.exini.dicom.data.DicomParts.{ DicomPart, MetaPart }
import com.exini.dicom.data.TestData._
import com.exini.dicom.data._
import com.exini.dicom.streams.DicomFlows._
import com.exini.dicom.streams.ModifyFlow._
import com.exini.dicom.streams.ParseFlow._
import com.exini.dicom.streams.TestUtils._
import org.scalatest.BeforeAndAfterAll
import org.scalatest.flatspec.AnyFlatSpecLike
import org.scalatest.matchers.should.Matchers
import java.io.File
import scala.concurrent.duration.DurationInt
import scala.concurrent.{ Await, ExecutionContextExecutor }
class DicomFlowsTest
extends TestKit(ActorSystem("DicomFlowsSpec"))
with AnyFlatSpecLike
with Matchers
with BeforeAndAfterAll {
implicit val ec: ExecutionContextExecutor = system.dispatcher
override def afterAll(): Unit = system.terminate()
"A print flow" should "not change incoming elements" in {
val bytes = preamble ++ fmiGroupLength(transferSyntaxUID()) ++ transferSyntaxUID() ++ personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(printFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
"The stop tag flow" should "stop reading data when a stop tag is reached" in {
val bytes = studyDate() ++ personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(stopTagFlow(Tag.PatientName))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "stop reading data when a tag number is higher than the stop tag" in {
val bytes = studyDate() ++ personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(stopTagFlow(Tag.StudyDate + 1))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "apply stop tag correctly also when preceded by sequence and ignore tags in sequences" in {
val bytes = studyDate() ++ sequence(Tag.DerivationCodeSequence) ++ item() ++ pixelData(
10
) ++ itemDelimitation() ++ sequenceDelimitation() ++ personNameJohnDoe() ++ pixelData(100)
val source = Source
.single(bytes)
.via(parseFlow)
.via(stopTagFlow(Tag.PatientName + 1))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectSequence(Tag.DerivationCodeSequence)
.expectItem()
.expectHeader(Tag.PixelData)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
"The DICOM group length discard filter" should "discard group length elements except 0002,0000" in {
val bytes = preamble ++ fmiGroupLength(transferSyntaxUID()) ++ transferSyntaxUID() ++ groupLength(
8,
studyDate().length
) ++ studyDate()
val source = Source
.single(bytes)
.via(parseFlow)
.via(groupLengthDiscardFilter)
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "discard group length elements except 0002,0000 when testing with dicom file" in {
val file = new File(getClass.getResource("../data/test001.dcm").toURI)
val source = FileIO
.fromPath(file.toPath)
.via(parseFlow)
.via(groupLengthDiscardFilter)
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.FileMetaInformationVersion)
.expectValueChunk()
}
"The DICOM file meta information discard filter" should "discard file meta informaton" in {
val bytes =
preamble ++ fmiGroupLength(transferSyntaxUID()) ++ transferSyntaxUID() ++ personNameJohnDoe() ++ studyDate()
val source = Source
.single(bytes)
.via(parseFlow)
.via(fmiDiscardFilter)
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "discard file meta information when testing with dicom files" in {
val file = new File(getClass.getResource("../data/test001.dcm").toURI)
val source = FileIO
.fromPath(file.toPath)
.via(parseFlow)
.via(fmiDiscardFilter)
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.SpecificCharacterSet)
.expectValueChunk()
.expectHeader(Tag.ImageType)
}
"The tag filter" should "filter elements in sequences" in {
val bytes = sequence(
Tag.DerivationCodeSequence
) ++ item() ++ studyDate() ++ personNameJohnDoe() ++ itemDelimitation() ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(tagFilter(tagPath => tagPath.tag != Tag.PatientName))
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.DerivationCodeSequence)
.expectItem()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectDicomComplete()
}
it should "filter elements not matching the condition" in {
val bytes = preamble ++ fmiGroupLength(
fmiVersion(),
transferSyntaxUID()
) ++ fmiVersion() ++ transferSyntaxUID() ++ personNameJohnDoe() ++ studyDate()
val source = Source
.single(bytes)
.via(parseFlow)
.via(tagFilter(tagPath => groupNumber(tagPath.tag) >= 8, _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "filter elements not matching the condition when testing with sample dicom files" in {
val file = new File(getClass.getResource("../data/test001.dcm").toURI)
val source = FileIO
.fromPath(file.toPath)
.via(parseFlow)
.via(tagFilter(tagPath => tagPath.tag == Tag.PatientName, _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
it should "filter elements matching the condition" in {
val bytes = preamble ++ fmiGroupLength(
fmiVersion(),
transferSyntaxUID()
) ++ fmiVersion() ++ transferSyntaxUID() ++ studyDate()
val source = Source
.single(bytes)
.via(parseFlow)
.via(tagFilter(tagPath => !isFileMetaInformation(tagPath.tag), _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "filter elements matching the deny condition when testing with sample dicom files" in {
val file = new File(getClass.getResource("../data/test001.dcm").toURI)
val source = FileIO
.fromPath(file.toPath)
.via(parseFlow)
.via(tagFilter(tagPath => !isFileMetaInformation(tagPath.tag), _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.SpecificCharacterSet)
.expectValueChunk()
.expectHeader(Tag.ImageType)
}
it should "filter leave the dicom file unchanged when deny condition does not match any elements" in {
val file = new File(getClass.getResource("../data/test001.dcm").toURI)
val source = FileIO
.fromPath(file.toPath)
.via(parseFlow)
.via(tagFilter(tagPath => !isPrivate(tagPath.tag)))
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.FileMetaInformationVersion)
.expectValueChunk()
}
"The allow filter" should "block all elements not on the allow list" in {
val bytes =
preamble ++ fmiGroupLength(transferSyntaxUID()) ++ transferSyntaxUID() ++ personNameJohnDoe() ++ studyDate()
val source = Source
.single(bytes)
.via(parseFlow)
.via(allowFilter(Set(TagTree.fromTag(Tag.StudyDate)), _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "only apply to elements in the root dataset when filter points to root dataset" in {
val bytes = sequence(
Tag.DerivationCodeSequence
) ++ item() ++ personNameJohnDoe() ++ studyDate() ++ itemDelimitation() ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(allowFilter(Set(TagTree.fromTag(Tag.StudyDate)), _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectDicomComplete()
}
it should "also work on fragments" in {
val bytes = pixeDataFragments() ++ item(4) ++ ByteString(1, 2, 3, 4) ++ item(4) ++
ByteString(5, 6, 7, 8) ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(allowFilter(Set.empty, _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectDicomComplete()
}
it should "preserve sequences and items in nested structures when using wildcards" in {
val bytes = personNameJohnDoe() ++ sequence(
Tag.DerivationCodeSequence
) ++ item() ++ personNameJohnDoe() ++ studyDate() ++ itemDelimitation() ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(allowFilter(Set(TagTree.fromAnyItem(Tag.DerivationCodeSequence).thenTag(Tag.StudyDate)), _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.DerivationCodeSequence)
.expectItem()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectDicomComplete()
}
it should "preserve sequences and items in nested structures when using item indices" in {
val bytes = personNameJohnDoe() ++ sequence(
Tag.DerivationCodeSequence
) ++ item() ++ personNameJohnDoe() ++ itemDelimitation() ++ item() ++ studyDate() ++ itemDelimitation() ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(allowFilter(Set(TagTree.fromItem(Tag.DerivationCodeSequence, 2).thenTag(Tag.StudyDate)), _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.DerivationCodeSequence)
.expectItem()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectDicomComplete()
}
"The deny filter" should "block the entire sequence when a sequence tag is on the deny list" in {
val bytes = studyDate() ++
(sequence(Tag.DerivationCodeSequence) ++ item() ++ personNameJohnDoe() ++
(sequence(
Tag.AbstractPriorCodeSequence
) ++ item() ++ personNameJohnDoe() ++ itemDelimitation() ++ sequenceDelimitation()) ++
itemDelimitation() ++ sequenceDelimitation()) ++
personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(denyFilter(Set(TagTree.fromAnyItem(Tag.DerivationCodeSequence)), _ => false))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
it should "block a single item inside a sequence" in {
val bytes = studyDate() ++
sequence(
Tag.DerivationCodeSequence
) ++ item() ++ personNameJohnDoe() ++ itemDelimitation() ++ item() ++ studyDate() ++ itemDelimitation() ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(
denyFilter(
Set(TagTree.fromTag(Tag.StudyDate), TagTree.fromItem(Tag.DerivationCodeSequence, 1)),
_ => false
)
)
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.DerivationCodeSequence)
.expectItem()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectDicomComplete()
}
it should "block an element in an item in a sequence" in {
val bytes = studyDate() ++
sequence(
Tag.DerivationCodeSequence
) ++ item() ++ personNameJohnDoe() ++ itemDelimitation() ++ item() ++ studyDate() ++ itemDelimitation() ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(denyFilter(Set(TagTree.fromItem(Tag.DerivationCodeSequence, 1).thenTag(Tag.StudyDate)), _ => true))
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectSequence(Tag.DerivationCodeSequence)
.expectItem()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectItemDelimitation()
.expectItem()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectDicomComplete()
}
"The header part filter" should "discard elements based on its header part" in {
val bytes =
studyDate() ++ sequence(Tag.DerivationCodeSequence) ++ item() ++ personNameJohnDoe() ++ itemDelimitation() ++
item() ++ studyDate() ++ itemDelimitation() ++ sequenceDelimitation() ++ personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(headerFilter(header => header.vr == VR.PN))
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.DerivationCodeSequence)
.expectItem()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectItemDelimitation()
.expectItem()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
"The context validation flow" should "accept DICOM data that corresponds to the given contexts" in {
val contexts = Seq(ValidationContext(UID.CTImageStorage, UID.ExplicitVRLittleEndian))
val bytes = preamble ++
fmiGroupLength(mediaStorageSOPClassUID() ++ mediaStorageSOPInstanceUID() ++ transferSyntaxUID()) ++
mediaStorageSOPClassUID() ++ mediaStorageSOPInstanceUID() ++ transferSyntaxUID()
val source = Source
.single(bytes)
.via(parseFlow)
.via(validateContextFlow(contexts))
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.MediaStorageSOPClassUID)
.expectValueChunk()
.expectHeader(Tag.MediaStorageSOPInstanceUID)
.expectValueChunk()
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectDicomComplete()
}
it should "accept SOP Class UID specified in either file meta information or in the dataset" in {
val contexts = Seq(ValidationContext(UID.CTImageStorage, UID.ExplicitVRLittleEndian))
val bytes = preamble ++
fmiGroupLength(mediaStorageSOPInstanceUID() ++ transferSyntaxUID()) ++
mediaStorageSOPInstanceUID() ++ transferSyntaxUID() ++ sopClassUID()
val source = Source
.single(bytes)
.via(parseFlow)
.via(validateContextFlow(contexts))
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.MediaStorageSOPInstanceUID)
.expectValueChunk()
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectHeader(Tag.SOPClassUID)
.expectValueChunk()
.expectDicomComplete()
}
it should "not accept DICOM data that does not correspond to the given contexts" in {
val contexts = Seq(ValidationContext(UID.CTImageStorage, "1.2.840.10008.1.2.2"))
val bytes = preamble ++
fmiGroupLength(
fmiVersion() ++ mediaStorageSOPClassUID() ++ mediaStorageSOPInstanceUID() ++ transferSyntaxUID()
) ++
fmiVersion() ++ mediaStorageSOPClassUID() ++ mediaStorageSOPInstanceUID() ++ transferSyntaxUID()
val source = Source
.single(bytes)
.via(parseFlow)
.via(validateContextFlow(contexts))
source
.runWith(TestSink.probe[DicomPart])
.expectDicomError()
}
it should "not accept a file with no SOPCLassUID if a context is given" in {
val contexts = Seq(ValidationContext(UID.CTImageStorage, UID.ExplicitVRLittleEndian))
val bytes = preamble ++
fmiGroupLength(fmiVersion() ++ mediaStorageSOPInstanceUID() ++ transferSyntaxUID()) ++
fmiVersion() ++ mediaStorageSOPInstanceUID() ++ transferSyntaxUID()
val source = Source
.single(bytes)
.via(parseFlow)
.via(validateContextFlow(contexts))
source
.runWith(TestSink.probe[DicomPart])
.expectDicomError()
}
it should "not accept a file with no TransferSyntaxUID if a context is given" in {
val contexts = Seq(ValidationContext(UID.CTImageStorage, UID.ExplicitVRLittleEndian))
val bytes = preamble ++
fmiGroupLength(fmiVersion() ++ mediaStorageSOPClassUID() ++ mediaStorageSOPInstanceUID()) ++
fmiVersion() ++ mediaStorageSOPClassUID() ++ mediaStorageSOPInstanceUID()
val source = Source
.single(bytes)
.via(parseFlow)
.via(validateContextFlow(contexts))
source
.runWith(TestSink.probe[DicomPart])
.expectDicomError()
}
it should "not accept DICOM data if no valid contexts are given" in {
val contexts = Seq()
val bytes = preamble ++
fmiGroupLength(
fmiVersion() ++ mediaStorageSOPClassUID() ++ mediaStorageSOPInstanceUID() ++ transferSyntaxUID()
) ++
fmiVersion() ++ mediaStorageSOPClassUID() ++ mediaStorageSOPInstanceUID() ++ transferSyntaxUID()
val source = Source
.single(bytes)
.via(parseFlow)
.via(validateContextFlow(contexts))
source
.runWith(TestSink.probe[DicomPart])
.expectDicomError()
}
"The deflate flow" should "recreate the dicom parts of a dataset which has been deflated and inflated again" in {
val bytes = fmiGroupLength(transferSyntaxUID()) ++ transferSyntaxUID() ++ personNameJohnDoe() ++ studyDate()
val source = Source
.single(bytes)
.via(parseFlow)
.via(
modifyFlow(modifications =
Seq(
TagModification.equals(
TagPath.fromTag(Tag.FileMetaInformationGroupLength),
_ => fmiGroupLength(transferSyntaxUID(UID.DeflatedExplicitVRLittleEndian)).drop(8)
),
TagModification
.equals(TagPath.fromTag(Tag.TransferSyntaxUID), _ => ByteString(UID.DeflatedExplicitVRLittleEndian))
)
)
)
.via(deflateDatasetFlow)
.map(_.bytes)
.via(parseFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "not deflate meta information" in {
val bytes = fmiGroupLength(transferSyntaxUID()) ++ transferSyntaxUID() ++ personNameJohnDoe() ++ studyDate()
val source = Source
.single(bytes)
.via(parseFlow)
.via(
modifyFlow(modifications =
Seq(
TagModification.equals(
TagPath.fromTag(Tag.FileMetaInformationGroupLength),
_ => fmiGroupLength(transferSyntaxUID(UID.DeflatedExplicitVRLittleEndian)).drop(8)
),
TagModification
.equals(TagPath.fromTag(Tag.TransferSyntaxUID), _ => ByteString(UID.DeflatedExplicitVRLittleEndian))
)
)
)
.via(deflateDatasetFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectDeflatedChunk()
}
it should "not deflate data with non-deflated transfer syntax" in {
val bytes = fmiGroupLength(transferSyntaxUID()) ++ transferSyntaxUID() ++ personNameJohnDoe() ++ studyDate()
val source = Source
.single(bytes)
.via(parseFlow)
.via(deflateDatasetFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectDicomComplete()
}
it should "not ouput bytes when the stream is empty" in {
val bytes = ByteString.empty
val source = Source
.single(bytes)
.via(parseFlow)
.via(deflateDatasetFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectDicomComplete()
}
"The bulk data filter flow" should "remove pixel data" in {
val bytes =
preamble ++ fmiGroupLength(transferSyntaxUID()) ++ transferSyntaxUID() ++ personNameJohnDoe() ++ pixelData(1000)
val source = Source
.single(bytes)
.via(parseFlow)
.via(bulkDataFilter)
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk()
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
it should "not remove pixel data in sequences" in {
val bytes = sequence(Tag.DerivationCodeSequence) ++ item() ++ personNameJohnDoe() ++ pixelData(
100
) ++ itemDelimitation() ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(bulkDataFilter)
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.DerivationCodeSequence)
.expectItem()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectHeader(Tag.PixelData)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectDicomComplete()
}
it should "only remove waveform data when inside waveform sequence" in {
val bytes = waveformSeqStart() ++ item() ++ personNameJohnDoe() ++ waveformData(
100
) ++ itemDelimitation() ++ sequenceDelimitation() ++ personNameJohnDoe() ++ waveformData(100)
val source = Source
.single(bytes)
.via(parseFlow)
.via(bulkDataFilter)
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.WaveformSequence)
.expectItem()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectHeader(Tag.WaveformData)
.expectValueChunk()
.expectDicomComplete()
}
it should "remove fragments data" in {
val bytes = personNameJohnDoe() ++ pixeDataFragments() ++ item(4) ++ ByteString(1, 2, 3, 4) ++ item(4) ++
ByteString(5, 6, 7, 8) ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(bulkDataFilter)
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
"The FMI group length flow" should "calculate and emit the correct group length attribute" in {
val correctLength = transferSyntaxUID().length
val bytes = preamble ++ fmiGroupLength(
fmiVersion(),
transferSyntaxUID()
) ++ fmiVersion() ++ transferSyntaxUID() ++ personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(denyFilter(Set(TagTree.fromTag(Tag.FileMetaInformationVersion)), _ => true))
.via(fmiGroupLengthFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk(intToBytesLE(correctLength))
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
it should "work also in flows with file meta information only" in {
val correctLength = transferSyntaxUID().length
val bytes = preamble ++ transferSyntaxUID() // missing file meta information group length
val source = Source
.single(bytes)
.via(parseFlow)
.via(fmiGroupLengthFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk(intToBytesLE(correctLength))
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectDicomComplete()
}
it should "work in flows without preamble" in {
val correctLength = transferSyntaxUID().length
val bytes = transferSyntaxUID() ++ personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(fmiGroupLengthFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk(intToBytesLE(correctLength))
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
it should "not emit anything in empty flows" in {
val bytes = ByteString.empty
val source = Source
.single(bytes)
.via(parseFlow)
.via(fmiGroupLengthFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectDicomComplete()
}
it should "not emit a group length attribute when there is no FMI" in {
val bytes = preamble ++ personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(fmiGroupLengthFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectPreamble()
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
it should "keep a zero length group length attribute" in {
val bytes = fmiGroupLength(ByteString.empty) ++ personNameJohnDoe()
val source = Source
.single(bytes)
.via(parseFlow)
.via(fmiGroupLengthFlow)
source
.runWith(TestSink.probe[DicomPart])
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk(ByteString(0, 0, 0, 0))
.expectHeader(Tag.PatientName)
.expectValueChunk()
.expectDicomComplete()
}
it should "ignore DICOM parts of unknown type" in {
case object SomePart extends MetaPart
val correctLength = transferSyntaxUID().length
val bytes = preamble ++ transferSyntaxUID() // missing file meta information group length
val source = Source
.single(bytes)
.via(parseFlow)
.prepend(Source.single(SomePart))
.via(fmiGroupLengthFlow)
source
.runWith(TestSink.probe[DicomPart])
.request(1)
.expectNextChainingPF {
case SomePart => true
}
.expectPreamble()
.expectHeader(Tag.FileMetaInformationGroupLength)
.expectValueChunk(intToBytesLE(correctLength))
.expectHeader(Tag.TransferSyntaxUID)
.expectValueChunk()
.expectDicomComplete()
}
"The sequence length filter" should "replace determinate length sequences and items with indeterminate, and insert delimitations" in {
val bytes =
sequence(Tag.DerivationCodeSequence, 56) ++ item(
16
) ++ studyDate() ++ item() ++ studyDate() ++ itemDelimitation() ++
sequence(Tag.AbstractPriorCodeSequence) ++ item() ++ studyDate() ++ itemDelimitation() ++ item(
16
) ++ studyDate() ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(toIndeterminateLengthSequences)
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.DerivationCodeSequence, indeterminateLength)
.expectItem(indeterminateLength)
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation() // inserted
.expectItem()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation() // inserted
.expectSequence(Tag.AbstractPriorCodeSequence, indeterminateLength)
.expectItem(indeterminateLength)
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation()
.expectItem()
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation() // inserted
.expectSequenceDelimitation()
.expectDicomComplete()
}
it should "handle sequences that end with an item delimitation" in {
val bytes =
sequence(Tag.DerivationCodeSequence, 32) ++ item() ++ studyDate() ++ itemDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(toIndeterminateLengthSequences)
source
.runWith(TestSink.probe[DicomPart])
.expectSequence(Tag.DerivationCodeSequence, indeterminateLength)
.expectItem(indeterminateLength)
.expectHeader(Tag.StudyDate)
.expectValueChunk()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectDicomComplete()
}
it should "should not remove length from items in fragments" in {
val bytes =
pixeDataFragments() ++ item(4) ++ ByteString(1, 2, 3, 4) ++ sequenceDelimitation() ++
sequence(Tag.DerivationCodeSequence, 40) ++ item(32) ++
pixeDataFragments() ++ item(4) ++ ByteString(1, 2, 3, 4) ++ sequenceDelimitation()
val source = Source
.single(bytes)
.via(parseFlow)
.via(toIndeterminateLengthSequences)
source
.runWith(TestSink.probe[DicomPart])
.expectFragments()
.expectItem(4)
.expectValueChunk()
.expectFragmentsDelimitation()
.expectSequence(Tag.DerivationCodeSequence, indeterminateLength)
.expectItem(indeterminateLength)
.expectFragments()
.expectItem(4)
.expectValueChunk()
.expectFragmentsDelimitation()
.expectItemDelimitation()
.expectSequenceDelimitation()
.expectDicomComplete()
}
it should "work in datasets with nested sequences" in {
val bytes = studyDate() ++ sequence(Tag.DerivationCodeSequence, 60) ++ item(52) ++ studyDate() ++
sequence(Tag.DerivationCodeSequence, 24) ++ item(16) ++ studyDate() ++ personNameJohnDoe()