# itk-image-pad-resample

> Resample virtually any type of image 2D, 3D with 1 or multiple components.

[![NPM](https://img.shields.io/npm/v/itk-image-pad-resample.svg)](https://www.npmjs.com/package/itk-image-pad-resample) [![JavaScript Style Guide](https://img.shields.io/badge/code_style-standard-brightgreen.svg)](https://standardjs.com)

## Install

Install with the flag '-g' and use it in the command line. 

```bash
npm install itk-image-pad-resample -g
```

## Usage in the command line

```bash
img-pad-resample --help
```

```
Help: Resample an image to a specific size.
Required:
--img <input path to image> or --dir <directory>
--size <sizeX,sizeY,sizeZ>

Optional:
--out <output path> default: out.nrrd
--out_ext <output extension> (when using --dir) default: .nrrd
--spacing <spacingX,spacingY,spacingZ> Input image spacing is used. Otherwise, is set to fit the output size.
--pad <padX,padY,padZ> pad output at the top
--iso_spacing If this is set, the spacing of the output image will be isometric, i.e., the same for all dimensions which means the max spacing value is selected and set for all dimensions.
--center_image If this is set, the output image is centered in the resampled space.
--linear Linear interpolation, default is nearest neighbor.
```

```bash
img-pad-resample --img /path/to/input.nii --size 250,250,250 --out temp.nrrd 
```

To process a whole directory with images

```bash
img-pad-resample --dir /path/to/directory --size 250,250 --out /path/to/output/dir --out_ext .jpg
```

## Usage in your js logic

Use [med-img-reader](https://www.npmjs.com/package/med-img-reader) to read any type of image with one or multiple
components in a variety of formats. 

```js
const MedImgReader = require('med-img-reader');
const ImgPadResampleLib = require('itk-image-pad-resample');
```

```js
const medimgreader = new MedImgReader();
medimgreader.SetFilename('/path/to/input{.png,.jpg,.nrrd,.nii.gz,.dcm}');
medimgreader.ReadImage();
const in_img = medimgreader.GetOutput();

const imgpad = new ImgPadResampleLib();
imgpad.SetImage(in_img);
imgpad.SetOutputSize([300, 250]);
imgpad.SetFitSpacingToOutputSizeOn(); //optional
imgpad.SetIsoSpacingOn(); //optional 
imgpad.SetCenterImageOn(); //optional
imgpad.SetInterpolationTypeToLinear(); //default is nearest
imgpad.Update();
var img_out = imgpad.GetOutput();

const writer = new MedImgReader();
writer.SetInput(img_out);
writer.SetFilename('/path/to/ouput/{.png,.jpg,.nrrd,.nii.gz,.dcm}');
writer.WriteImage();

```

## Example

Input RGBA image: 
![alt text](https://github.com/juanprietob/itk-image-pad-resample/raw/master/test/brain.png "Brain image with multiple components (RGB)")

```bash
img-pad-resample --img brain.png --size 500,250 --out out_brain.png 
```

Output RGBA image, the image here might look stretched because typical image viewers will not take spacing information in consideration!: 
![alt text](https://github.com/juanprietob/itk-image-pad-resample/raw/master/test/out_brain.png "Image with different spacing")


Use flag '--iso_spacing' to have the same spacing in all dimensions
```bash
img-pad-resample --img brain.png --size 500,250 --iso_spacing --out out_brain_iso.png 
```

Output RGBA image with equal spacing: 
![alt text](https://github.com/juanprietob/itk-image-pad-resample/raw/master/test/out_brain_iso.png "Image with equal spacing")

## Convert image to a tensorflow Tensor [tfjs](https://www.tensorflow.org/js)

---
	const tf = require('@tensorflow/tfjs-node');//Or tfjs in browser or tfjs-node-gpu if in linux

	tf.tensor(
		Float32Array.from(img_out.data), 
		[1, ...[...img_out.size].reverse(), img_out.imageType.components]
	));
---

## License

MIT © [juanprietob](https://github.com/juanprietob)