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Feature/various updates #26

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merged 3 commits into from
Feb 1, 2021
Merged

Feature/various updates #26

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42d15f9
Added uid to name lookup
karl-exini Jan 30, 2021
6892d7f
Removed indices from items and fragments during parsing
karl-exini Jan 31, 2021
9c42dab
Fixed handling of cp246 sequences
karl-exini Feb 1, 2021
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12 changes: 3 additions & 9 deletions src/collect-flow.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -111,12 +111,7 @@ export function collectFlow(
}

if (part instanceof ItemPart && this.inFragments) {
this.currentFragment = new FragmentElement(
part.index,
part.length,
Value.empty(),
part.bigEndian,
);
this.currentFragment = new FragmentElement(part.length, Value.empty(), part.bigEndian);
this.bytes = emptyBuffer;
return [];
}
Expand All @@ -127,7 +122,6 @@ export function collectFlow(
if (this.inFragments && this.currentFragment) {
this.maybeAdd(
new FragmentElement(
this.currentFragment.index,
this.currentFragment.length,
new Value(this.bytes),
this.currentFragment.bigEndian,
Expand Down Expand Up @@ -160,14 +154,14 @@ export function collectFlow(
return [];
}
if (part instanceof ItemPart) {
this.maybeAdd(new ItemElement(part.index, part.length, part.bigEndian));
this.maybeAdd(new ItemElement(part.length, part.bigEndian));
return [];
}
if (part instanceof ItemDelimitationPartMarker) {
return [];
}
if (part instanceof ItemDelimitationPart) {
this.maybeAdd(new ItemDelimitationElement(part.index, part.bigEndian));
this.maybeAdd(new ItemDelimitationElement(part.bigEndian));
return [];
}
if (part === sequenceDelimitationPartMarker) {
Expand Down
92 changes: 43 additions & 49 deletions src/dicom-elements.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -109,18 +109,17 @@ export class ValueElement extends ElementSet {
const vm = strings.length + '';
return (
'ValueElement(' +
tagToString(this.tag) +
' ' +
this.vr.name +
' [' +
s +
'] # ' +
this.length +
', ' +
vm +
' ' +
Lookup.keywordOf(this.tag) +
')'
tagToString(this.tag) +
' ' +
this.vr.name +
' [' +
s +
'] # ' +
this.length +
', ' +
vm +
' ' +
Lookup.keywordOf(this.tag) || '' + ')'
);
}
}
Expand All @@ -147,7 +146,8 @@ export class SequenceElement extends Element {
}
public toString(): string {
return (
'SequenceElement(' + tagToString(this.tag) + ' SQ # ' + this.length + ' ' + Lookup.keywordOf(this.tag) + ')'
'SequenceElement(' + tagToString(this.tag) + ' SQ # ' + this.length + ' ' + Lookup.keywordOf(this.tag) ||
'' + ')'
);
}
}
Expand Down Expand Up @@ -179,15 +179,16 @@ export class FragmentsElement extends Element {
}
public toString(): string {
return (
'FragmentsElement(' + tagToString(this.tag) + ' ' + this.vr.name + ' # ' + Lookup.keywordOf(this.tag) + ')'
'FragmentsElement(' + tagToString(this.tag) + ' ' + this.vr.name + ' # ' + Lookup.keywordOf(this.tag) ||
'' + ')'
);
}
}

export class ItemElement extends Element {
public indeterminate: boolean;

constructor(public readonly index: number, public readonly length = indeterminateLength, bigEndian?: boolean) {
constructor(public readonly length = indeterminateLength, bigEndian?: boolean) {
super(bigEndian);
this.indeterminate = this.length === indeterminateLength;
}
Expand All @@ -196,20 +197,15 @@ export class ItemElement extends Element {
return concat(tagToBytes(Tag.Item, this.bigEndian), intToBytes(this.length, this.bigEndian));
}
public toParts(): DicomPart[] {
return [new ItemPart(this.index, this.length, this.bigEndian, this.toBytes())];
return [new ItemPart(this.length, this.bigEndian, this.toBytes())];
}
public toString(): string {
return 'ItemElement(index = ' + this.index + ', length = ' + this.length + ')';
return 'ItemElement(length = ' + this.length + ')';
}
}

export class FragmentElement extends Element {
constructor(
public readonly index: number,
public readonly length: number,
public readonly value: Value,
bigEndian?: boolean,
) {
constructor(public readonly length: number, public readonly value: Value, bigEndian?: boolean) {
super(bigEndian);
}

Expand All @@ -219,30 +215,30 @@ export class FragmentElement extends Element {
.reduce(concat);
}
public toParts(): DicomPart[] {
const itemParts: DicomPart[] = new ItemElement(this.index, this.value.length, this.bigEndian).toParts();
const itemParts: DicomPart[] = new ItemElement(this.value.length, this.bigEndian).toParts();
if (this.value.length !== 0) {
itemParts.push(new ValueChunk(this.bigEndian, this.value.bytes, true));
}
return itemParts;
}
public toString(): string {
return 'FragmentElement(index = ' + this.index + ', length = ' + this.length + ')';
return 'FragmentElement(length = ' + this.length + ')';
}
}

export class ItemDelimitationElement extends Element {
constructor(public readonly index: number, bigEndian?: boolean) {
constructor(bigEndian?: boolean) {
super(bigEndian);
}

public toBytes(): Buffer {
return concat(tagToBytes(Tag.ItemDelimitationItem, this.bigEndian), Buffer.from([0, 0, 0, 0]));
}
public toParts(): DicomPart[] {
return [new ItemDelimitationPart(this.index, this.bigEndian, this.toBytes())];
return [new ItemDelimitationPart(this.bigEndian, this.toBytes())];
}
public toString(): string {
return 'ItemDelimitationElement(index = ' + this.index + ')';
return 'ItemDelimitationElement';
}
}

Expand Down Expand Up @@ -301,7 +297,7 @@ export class Sequence extends ElementSet {
const elements = [];
elements.push(new SequenceElement(this.tag, this.length, this.bigEndian, this.explicitVR));
for (let i = 1; i <= this.items.length; i++) {
const itemElements = this.item(i).toElements(i);
const itemElements = this.item(i).toElements();
itemElements.forEach((e) => elements.push(e));
}
if (this.indeterminate) {
Expand All @@ -317,14 +313,13 @@ export class Sequence extends ElementSet {
public toString(): string {
return (
'Sequence(' +
tagToString(this.tag) +
' SQ # ' +
this.length +
' ' +
this.size +
' ' +
Lookup.keywordOf(this.tag) +
')'
tagToString(this.tag) +
' SQ # ' +
this.length +
' ' +
this.size +
' ' +
Lookup.keywordOf(this.tag) || '' + ')'
);
}
}
Expand All @@ -340,17 +335,17 @@ export class Item {
this.indeterminate = length === indeterminateLength;
}

public toElements(index: number): Element[] {
public toElements(): Element[] {
const elements: Element[] = [];
elements.push(new ItemElement(index, this.length, this.bigEndian));
elements.push(new ItemElement(this.length, this.bigEndian));
this.elements.toElements(false).forEach((e) => elements.push(e));
if (this.indeterminate) {
elements.push(new ItemDelimitationElement(index, this.bigEndian));
elements.push(new ItemDelimitationElement(this.bigEndian));
}
return elements;
}
public toBytes(): Buffer {
return this.toElements(1)
return this.toElements()
.map((e) => e.toBytes())
.reduce(concat);
}
Expand All @@ -370,8 +365,8 @@ export class Fragment {
public readonly bigEndian: boolean = false,
) {}

public toElement(index: number): Element {
return new FragmentElement(index, this.length, this.value, this.bigEndian);
public toElement(): Element {
return new FragmentElement(this.length, this.value, this.bigEndian);
}
public toString(): string {
return 'Fragment(length = ' + this.length + ', value length = ' + this.value.length + ')';
Expand Down Expand Up @@ -434,7 +429,6 @@ export class Fragments extends ElementSet {
if (this.offsets !== undefined) {
elements.push(
new FragmentElement(
1,
4 * this.offsets.length,
new Value(
this.offsets
Expand All @@ -445,10 +439,10 @@ export class Fragments extends ElementSet {
),
);
} else {
elements.push(new FragmentElement(1, 0, Value.empty()));
elements.push(new FragmentElement(0, Value.empty()));
}
for (let i = 1; i <= this.fragments.length; i++) {
elements.push(this.fragment(i).toElement(i + 1));
elements.push(this.fragment(i).toElement());
}
elements.push(new SequenceDelimitationElement(this.bigEndian));
return elements;
Expand All @@ -459,8 +453,8 @@ export class Fragments extends ElementSet {
return new Fragments(this.tag, this.vr, this.offsets, newFragments, this.bigEndian, this.explicitVR);
}
public toString(): string {
return `Fragments(${tagToString(this.tag)} ${this.vr.name} # ${this.fragments.length} ${Lookup.keywordOf(
this.tag,
)})`;
return `Fragments(${tagToString(this.tag)} ${this.vr.name} # ${this.fragments.length} ${
Lookup.keywordOf(this.tag) || ''
})`;
}
}
23 changes: 15 additions & 8 deletions src/dicom-flow.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ import {
ValueChunk,
} from './dicom-parts';
import { Tag } from './tag';
import { emptyTagPath, TagPath, TagPathItem } from './tag-path';
import { emptyTagPath, TagPath, TagPathItem, TagPathItemEnd } from './tag-path';

export function createFlow(flow: any): any {
return pipe(flow.baseFlow(), flatMapFlow(flow.handlePart.bind(flow)));
Expand Down Expand Up @@ -241,14 +241,15 @@ class SequenceDelimitationPartMarker extends SequenceDelimitationPart {
export const sequenceDelimitationPartMarker = new SequenceDelimitationPartMarker();

export class ItemDelimitationPartMarker extends ItemDelimitationPart {
constructor(index: number) {
super(index, false, emptyBuffer);
constructor() {
super(false, emptyBuffer);
}

public toString(): string {
return 'ItemDelimitationMarker []';
}
}
export const itemDelimitationPartMarker = new ItemDelimitationPartMarker();

/**
* Depends on InFragments
Expand Down Expand Up @@ -315,7 +316,7 @@ export const GuaranteedDelimitationEvents = (Super: any): any =>
this.partStack = this.partStack.slice(splitIndex);
const out = inactive.map((i) =>
i.part instanceof ItemPart
? this.onItemDelimitation(new ItemDelimitationPartMarker((i.part as ItemPart).index))
? this.onItemDelimitation(itemDelimitationPartMarker)
: this.onSequenceDelimitation(sequenceDelimitationPartMarker),
);
return [].concat(...out);
Expand All @@ -333,18 +334,20 @@ export const InSequence = (Super: any): any =>
class extends Super {
public sequenceStack: SequencePart[] = [];

public sequenceDepth() {
public sequenceDepth(): number {
return this.sequenceStack.length;
}
public inSequence() {
public inSequence(): boolean {
return this.sequenceStack.length > 0;
}
public onSequence(part: SequencePart): DicomPart[] {
this.sequenceStack.unshift(part);
return super.onSequence(part);
}
public onSequenceDelimitation(part: SequenceDelimitationPart): DicomPart[] {
this.sequenceStack.shift();
if (!this.inFragments) {
this.sequenceStack.shift();
}
return super.onSequenceDelimitation(part);
}
};
Expand Down Expand Up @@ -381,7 +384,11 @@ export const TagPathTracking = (Super: any): any =>
public onItem(part: ItemPart): DicomPart[] {
const t = this.tagPath;
if (!this.inFragments) {
this.tagPath = t.previous().thenItem(t.tag(), part.index);
if (t instanceof TagPathItemEnd) {
this.tagPath = t.previous().thenItem(t.tag(), t.item + 1);
} else {
this.tagPath = t.previous().thenItem(t.tag(), 1);
}
}
return super.onItem(part);
}
Expand Down
3 changes: 1 addition & 2 deletions src/dicom-flows.ts
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Expand Up @@ -311,7 +311,6 @@ export function toIndeterminateLengthSequences(): any {
return super.onItem(part).map((p: DicomPart) => {
if (p instanceof ItemPart && !this.inFragments && !p.indeterminate) {
return new ItemPart(
part.index,
indeterminateLength,
part.bigEndian,
concat(part.bytes.slice(0, part.bytes.length - 4), this.indeterminateBytes),
Expand All @@ -324,7 +323,7 @@ export function toIndeterminateLengthSequences(): any {
public onItemDelimitation(part: ItemDelimitationPart): DicomPart[] {
const out = super.onItemDelimitation(part);
if (part.bytes.length <= 0) {
out.push(new ItemDelimitationPart(part.index, part.bigEndian, itemDelimitation(part.bigEndian)));
out.push(new ItemDelimitationPart(part.bigEndian, itemDelimitation(part.bigEndian)));
}
return out;
}
Expand Down
8 changes: 4 additions & 4 deletions src/dicom-parts.ts
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Expand Up @@ -149,23 +149,23 @@ export class DeflatedChunk extends DicomPart {
export class ItemPart extends DicomPart {
public indeterminate = false;

constructor(public readonly index: number, public readonly length: number, bigEndian: boolean, bytes: Buffer) {
constructor(public readonly length: number, bigEndian: boolean, bytes: Buffer) {
super(bigEndian, bytes);
this.indeterminate = length === indeterminateLength;
}

public toString(): string {
return 'Item [length = ' + this.length + ', index = ' + this.index + ']';
return 'Item [length = ' + this.length + ']';
}
}

export class ItemDelimitationPart extends DicomPart {
constructor(public readonly index: number, bigEndian: boolean, bytes: Buffer) {
constructor(bigEndian: boolean, bytes: Buffer) {
super(bigEndian, bytes);
}

public toString(): string {
return 'ItemDelimitation [index = ' + this.index + ']';
return 'ItemDelimitation';
}
}

Expand Down
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