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Merge pull request #14 from slicebox/release-0-1-1
Moved Dicom parts to DicomParts, added some utils for attributes
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106 changes: 106 additions & 0 deletions
106
src/main/scala/se/nimsa/dcm4che/streams/DicomParts.scala
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,106 @@ | ||
| /* | ||
| * Copyright 2017 Lars Edenbrandt | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
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| package se.nimsa.dcm4che.streams | ||
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| import akka.util.ByteString | ||
| import org.dcm4che3.data.{SpecificCharacterSet, VR} | ||
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| object DicomParts { | ||
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| trait DicomPart { | ||
| def bigEndian: Boolean | ||
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| def bytes: ByteString | ||
| } | ||
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| case class DicomPreamble(bytes: ByteString) extends DicomPart { | ||
| def bigEndian = false | ||
| } | ||
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| case class DicomHeader(tag: Int, vr: VR, length: Int, isFmi: Boolean, bigEndian: Boolean, explicitVR: Boolean, bytes: ByteString) extends DicomPart { | ||
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| def withUpdatedLength(newLength: Int) : DicomHeader = { | ||
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| val updated = if ((bytes.size >= 8) && (explicitVR) && (vr.headerLength == 8)) { //explicit vr | ||
| bytes.take(6) ++ DicomParsing.shortToBytes(newLength.toShort, bigEndian) | ||
| } else if ((bytes.size >= 12) && (explicitVR) && (vr.headerLength == 12)) { //explicit vr | ||
| bytes.take(8) ++ DicomParsing.intToBytes(newLength, bigEndian) | ||
| } else { //implicit vr | ||
| bytes.take(4) ++ DicomParsing.intToBytes(newLength, bigEndian) | ||
| } | ||
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| DicomHeader(tag, vr, newLength, isFmi, bigEndian, explicitVR, updated) | ||
| } | ||
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| } | ||
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| case class DicomValueChunk(bigEndian: Boolean, bytes: ByteString, last: Boolean) extends DicomPart | ||
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| case class DicomDeflatedChunk(bigEndian: Boolean, bytes: ByteString) extends DicomPart | ||
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| case class DicomItem(length: Int, bigEndian: Boolean, bytes: ByteString) extends DicomPart | ||
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| case class DicomItemDelimitation(bigEndian: Boolean, bytes: ByteString) extends DicomPart | ||
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| case class DicomSequence(tag: Int, bigEndian: Boolean, bytes: ByteString) extends DicomPart | ||
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| case class DicomSequenceDelimitation(bigEndian: Boolean, bytes: ByteString) extends DicomPart | ||
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| case class DicomFragments(tag: Int, vr: VR, bigEndian: Boolean, bytes: ByteString) extends DicomPart | ||
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| case class DicomFragmentsDelimitation(bigEndian: Boolean, bytes: ByteString) extends DicomPart | ||
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| case class DicomUnknownPart(bigEndian: Boolean, bytes: ByteString) extends DicomPart | ||
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| case class DicomFragment(bigEndian: Boolean, valueChunks: Seq[DicomValueChunk]) extends DicomPart { | ||
| def bytes = valueChunks.map(_.bytes).fold(ByteString.empty)(_ ++ _) | ||
| } | ||
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| case class DicomAttribute(header: DicomHeader, valueChunks: Seq[DicomValueChunk]) extends DicomPart { | ||
| def bytes = valueChunks.map(_.bytes).fold(ByteString.empty)(_ ++ _) | ||
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| def bigEndian = header.bigEndian | ||
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| // LO: long string 64 chars max | ||
| // SH: short string 16 chars max | ||
| // PN: person name | ||
| // UI: 64 chars max | ||
| def withUpdatedStringValue(newValue: String, cs: SpecificCharacterSet = SpecificCharacterSet.ASCII): DicomAttribute = { | ||
| val newBytes = header.vr.toBytes(newValue, cs) | ||
| val needsPadding = newBytes.size % 2 == 1 | ||
| val newLength = if (needsPadding) newBytes.size + 1 else newBytes.size | ||
| val updatedHeader = header.withUpdatedLength(newLength.toShort) | ||
| val updatedValue = if (needsPadding) { | ||
| ByteString.fromArray(newBytes :+ header.vr.paddingByte().toByte) | ||
| } else { | ||
| ByteString.fromArray(newBytes) | ||
| } | ||
| DicomAttribute(updatedHeader, Seq(DicomValueChunk(header.bigEndian, updatedValue, true))) | ||
| } | ||
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| // DA: A string of characters of the format YYYYMMDD, 8 bytes fixed | ||
| def withUpdatedDateValue(newValue: String, cs: SpecificCharacterSet = SpecificCharacterSet.ASCII): DicomAttribute = { | ||
| val newBytes = header.vr.toBytes(newValue, cs) | ||
| val updatedValue = ByteString.fromArray(newBytes) | ||
| DicomAttribute(header, Seq(DicomValueChunk(header.bigEndian, updatedValue, true))) | ||
| } | ||
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| def asDicomParts: Seq[DicomPart] = header +: valueChunks | ||
| } | ||
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| } |
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65 changes: 65 additions & 0 deletions
65
src/test/scala/se/nimsa/dcm4che/streams/DicomPartsTest.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| package se.nimsa.dcm4che.streams | ||
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| import org.scalatest.{FlatSpecLike, Matchers} | ||
| import DicomData._ | ||
| import akka.util.ByteString | ||
| import se.nimsa.dcm4che.streams.DicomParts.{DicomAttribute, DicomHeader, DicomValueChunk} | ||
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| class DicomPartsTest extends FlatSpecLike with Matchers { | ||
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| "DicomHeader" should "should return a new header with modified length for explicitVR, LE" in { | ||
| val (tag, vr, headerLength, length) = DicomParsing.readHeaderExplicitVR(patientNameJohnDoe, false).get | ||
| val header = DicomHeader(tag, vr, length, false, false, true, patientNameJohnDoe.take(8)) | ||
| val updatedHeader = header.withUpdatedLength(5) | ||
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| updatedHeader.length shouldEqual 5 | ||
| updatedHeader.bytes.take(6) shouldEqual header.bytes.take(6) | ||
| updatedHeader.bytes(6) shouldEqual 5 | ||
| updatedHeader.bytes(7) shouldEqual 0 | ||
| } | ||
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| it should "should return a new header with modified length for explicitVR, BE" in { | ||
| val (tag, vr, headerLength, length) = DicomParsing.readHeaderExplicitVR(patientNameJohnDoeBE, true).get | ||
| val header = DicomHeader(tag, vr, length, false, true, true, patientNameJohnDoeBE.take(8)) | ||
| val updatedHeader = header.withUpdatedLength(5) | ||
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| updatedHeader.length shouldEqual 5 | ||
| updatedHeader.bytes.take(6) shouldEqual header.bytes.take(6) | ||
| updatedHeader.bytes(6) shouldEqual 0 | ||
| updatedHeader.bytes(7) shouldEqual 5 | ||
| } | ||
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| it should "should return a new header with modified length for implicitVR, LE" in { | ||
| val (tag, vr, headerLength, length) = DicomParsing.readHeaderImplicitVR(patientNameJohnDoeImplicit).get | ||
| val header = DicomHeader(tag, vr, length, false, false, false, patientNameJohnDoeImplicit.take(8)) | ||
| val updatedHeader = header.withUpdatedLength(5) | ||
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| updatedHeader.length shouldEqual 5 | ||
| updatedHeader.bytes.take(4) shouldEqual header.bytes.take(4) | ||
| updatedHeader.bytes(4) shouldEqual 5 | ||
| updatedHeader.bytes(5) shouldEqual 0 | ||
| } | ||
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| "DicomAttribute" should "should return a new attribute with updated header and updated value" in { | ||
| val (tag, vr, headerLength, length) = DicomParsing.readHeaderExplicitVR(patientNameJohnDoe, false).get | ||
| val header = DicomHeader(tag, vr, length, false, false, true, patientNameJohnDoe.take(8)) | ||
| val value = DicomValueChunk(false, patientNameJohnDoe.drop(8) ,true) | ||
| val attribute = DicomAttribute(header, Seq(value)) | ||
| val updatedAttribute = attribute.withUpdatedStringValue("Jimmyboy^Doe") | ||
| updatedAttribute.bytes.size shouldEqual 12 | ||
| updatedAttribute.header.length shouldEqual 12 | ||
| } | ||
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| it should "should return a new attribute with updated header and updated value with padding" in { | ||
| val (tag, vr, headerLength, length) = DicomParsing.readHeaderExplicitVR(patientNameJohnDoe, false).get | ||
| val header = DicomHeader(tag, vr, length, false, false, true, patientNameJohnDoe.take(8)) | ||
| val value = DicomValueChunk(false, patientNameJohnDoe.drop(8) ,true) | ||
| val attribute = DicomAttribute(header, Seq(value)) | ||
| val updatedAttribute = attribute.withUpdatedStringValue("Jimmy^Doe") | ||
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| updatedAttribute.bytes.size shouldEqual 10 | ||
| updatedAttribute.header.length shouldEqual 10 | ||
| updatedAttribute.bytes.drop(9) shouldEqual ByteString(32) | ||
| } | ||
| } |