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DOC: Update javascript API and add app, docs links #117

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132 changes: 132 additions & 0 deletions wasm/typescript/README.md
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# @itk-wasm/morphological-contour-interpolation

- 👨‍💻 [`Live API Demo`](https://kitwaremedical.github.io/ITKMorphologicalContourInterpolation/ts/app/) ✨
- 🕮 [`JavaScript Documentation`](https://kitwaremedical.github.io/ITKMorphologicalContourInterpolation/ts/docs/) 📚

[![npm version](https://badge.fury.io/js/@itk-wasm%2Fmorphological-contour-interpolation.svg)](https://www.npmjs.com/package/@itk-wasm/morphological-contour-interpolation)

> Morphology-based approach for interslice interpolation of anatomical slices from volumetric images.

## Installation

```sh
npm install @itk-wasm/morphological-contour-interpolation
```

## Usage

### Browser interface

Import:

```js
import {
morphologicalContourInterpolation,
setPipelinesBaseUrl,
getPipelinesBaseUrl,
} from "@itk-wasm/morphological-contour-interpolation"
```

#### morphologicalContourInterpolation

*Interpolates contours between slices.*

```ts
async function morphologicalContourInterpolation(
inputImage: Image,
options: MorphologicalContourInterpolationOptions = {}
) : Promise<MorphologicalContourInterpolationResult>
```

| Parameter | Type | Description |
| :----------: | :-----: | :-------------- |
| `inputImage` | *Image* | The input image |

**`MorphologicalContourInterpolationOptions` interface:**

| Property | Type | Description |
| :-------------------------: | :-------------------------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `label` | *number* | The label to interpolate. Interpolates all labels if set to 0 (default). |
| `axis` | *number* | Interpolate only along this axis. Interpolates along all axes if set to -1 (default). |
| `noHeuristicAlignment` | *boolean* | Heuristic alignment of regions for interpolation is faster than optimal alignment. |
| `noUseDistanceTransform` | *boolean* | Using distance transform instead of repeated dilations to calculate the median contour is slightly faster, but produces lower quality interpolations. |
| `useCustomSlicePositions` | *boolean* | Use custom slice positions (not slice auto-detection). |
| `noUseExtrapolation` | *boolean* | Perform extrapolation for branch extremities. Branch extremities are defined as regions having no overlap with any region in the next slice. Extrapolation helps generate smooth surface closings. |
| `useBallStructuringElement` | *boolean* | Use ball instead of default cross structuring element for repeated dilations. |
| `labeledSliceIndicesAxis` | *number* | Axis along which the labeled slice indices are defined. Default is -1 (that is, auto-detection). |
| `labeledSliceIndicesLabel` | *number* | Label of the slice indices. Default is 1. |
| `labeledSliceIndices` | *number[]* | List of labeled slice indices. Default is empty. |
| `webWorker` | *null or Worker or boolean* | WebWorker for computation. Set to null to create a new worker. Or, pass an existing worker. Or, set to `false` to run in the current thread / worker. |
| `noCopy` | *boolean* | When SharedArrayBuffer's are not available, do not copy inputs. |

**`MorphologicalContourInterpolationResult` interface:**

| Property | Type | Description |
| :-----------: | :------: | :------------------------------ |
| `outputImage` | *Image* | The output image |
| `webWorker` | *Worker* | WebWorker used for computation. |

#### setPipelinesBaseUrl

*Set base URL for WebAssembly assets when vendored.*

```ts
function setPipelinesBaseUrl(
baseUrl: string | URL
) : void
```

#### getPipelinesBaseUrl

*Get base URL for WebAssembly assets when vendored.*

```ts
function getPipelinesBaseUrl() : string | URL
```


### Node interface

Import:

```js
import {
morphologicalContourInterpolationNode,
} from "@itk-wasm/morphological-contour-interpolation"
```

#### morphologicalContourInterpolationNode

*Interpolates contours between slices.*

```ts
async function morphologicalContourInterpolationNode(
inputImage: Image,
options: MorphologicalContourInterpolationNodeOptions = {}
) : Promise<MorphologicalContourInterpolationNodeResult>
```

| Parameter | Type | Description |
| :----------: | :-----: | :-------------- |
| `inputImage` | *Image* | The input image |

**`MorphologicalContourInterpolationNodeOptions` interface:**

| Property | Type | Description |
| :-------------------------: | :--------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `label` | *number* | The label to interpolate. Interpolates all labels if set to 0 (default). |
| `axis` | *number* | Interpolate only along this axis. Interpolates along all axes if set to -1 (default). |
| `noHeuristicAlignment` | *boolean* | Heuristic alignment of regions for interpolation is faster than optimal alignment. |
| `noUseDistanceTransform` | *boolean* | Using distance transform instead of repeated dilations to calculate the median contour is slightly faster, but produces lower quality interpolations. |
| `useCustomSlicePositions` | *boolean* | Use custom slice positions (not slice auto-detection). |
| `noUseExtrapolation` | *boolean* | Perform extrapolation for branch extremities. Branch extremities are defined as regions having no overlap with any region in the next slice. Extrapolation helps generate smooth surface closings. |
| `useBallStructuringElement` | *boolean* | Use ball instead of default cross structuring element for repeated dilations. |
| `labeledSliceIndicesAxis` | *number* | Axis along which the labeled slice indices are defined. Default is -1 (that is, auto-detection). |
| `labeledSliceIndicesLabel` | *number* | Label of the slice indices. Default is 1. |
| `labeledSliceIndices` | *number[]* | List of labeled slice indices. Default is empty. |

**`MorphologicalContourInterpolationNodeResult` interface:**

| Property | Type | Description |
| :-----------: | :-----: | :--------------- |
| `outputImage` | *Image* | The output image |
2 changes: 1 addition & 1 deletion wasm/typescript/package.json
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{
"name": "@itk-wasm/morphological-contour-interpolation",
"version": "1.0.0",
"version": "1.0.1",
"packageManager": "[email protected]",
"description": "N-D morphology-based approach for interslice interpolation of anatomical slices from volumetric images.",
"type": "module",
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