#@script(env="/Users/username/.local/share/appose/fiji-cellpose/pixi.toml")

import cellpose
from cellpose import models
import numpy

#@Img image
#@output Img masks
#@output Img flows
print(image.shape)
print(numpy.sum(image))
model = models.CellposeModel(gpu=True)
masks, flows, _ = model.eval(image, z_axis=0, do_3D=False, normalize=True, diameter=150)

flows = flows[0]
flows = numpy.rollaxis(flows, -1)

import org.apposed.appose.*;
import java.util.*;

public class ApposeBuilder{
    //Toml to create a cellpose environment.
    static final String toml = """
[workspace]
    authors = [
                "Smith, MB",     
                ]
    channels = ["conda-forge"]
    name = "example-appose"
    platforms = ["osx-arm64", "win-64", "linux-64", "osx-64"]
    version = "0.1.0"
                
                [dependencies]
                python = ">3.10.3"
                
                [pypi-dependencies]
                cellpose = ">=4"
                appose = ">=0.10.1"
""";
    final static String command = """
import cellpose, sys, pathlib

ex = pathlib.Path(sys.executable)
#I could use this value with "wrap"
env = ex.parent.parent
#I can use this value with script parameter.
toml = env.parent.parent.parent / "pixi.toml"
"%s"%(toml, )
""";

	public static void main(String[] args) throws Exception{
	    try( Service python = Appose.pixi().content(toml).build().python() ){
            Map<String, Object> inputs = new HashMap<>();
            Service.Task task = python.task(command, inputs);
            task.start();
            task.waitFor();
            System.out.println(task.result());
        } 
	}
}