itk-image-pad-resample

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

Install

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

npm install itk-image-pad-resample -g

Usage in the command line

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.

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

To process a whole directory with images

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 to read any type of image with one or multiple components in a variety of formats.

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

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:

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!:

Use flag '--iso_spacing' to have the same spacing in all dimensions

img-pad-resample --img brain.png --size 500,250 --iso_spacing --out out_brain_iso.png 

Output RGBA image with equal spacing:

Convert image to a tensorflow Tensor tfjs

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