visualization-demo.imjoy.html

<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>

<config lang="json">
{
  "name": "ITK-VTK-Viewer",
  "type": "native-python",
  "version": "0.1.0",
  "description": "[TODO: describe this plugin with one sentence.]",
  "tags": [],
  "ui": "",
  "cover": "",
  "inputs": null,
  "outputs": null,
  "flags": [],
  "icon": "extension",
  "api_version": "0.1.8",
  "env": "",
  "permissions": [],
  "requirements": ["itk", "itkwidgets", "imageio", "tifffile"],
  "dependencies": []
}
</config>

<script lang="python">
# Run `pip install itk itkwidgets` before trying this example
from imjoy import api
import numpy as np
import itk
from itkwidgets.trait_types import itkimage_to_json, itkimage_from_json
from itkwidgets._transform_types import to_itk_image
from tifffile import imread

# register an encoder for encoding the itk.Image, the name `itkimage` will be used for decoding
# this example only use the encoder part
api.registerCodec({'name': 'itkimage', 'type': itk.Image, 'encoder': itkimage_to_json, 'decoder': itkimage_from_json})

class ImJoyPlugin():
    def setup(self):
        api.log('plugin initialized')

    async def run(self, ctx):
        files = await api.showFileDialog()
        # load the image data and inspect its shape
        membranes = imread(files[0].path)
        # image_array = np.random.randint(0, 255, [10,10,10], dtype='uint8')
        itk_image = to_itk_image(membranes)
        # here the itk_image will be encoded via the registered encoder function (i.e.: itkimage_to_json)
        api.createWindow(type="itk-vtk-viewer", src="https://oeway.github.io/itk-vtk-viewer/", data={"image_array": itk_image})

api.export(ImJoyPlugin())
</script>