Cellpose4.java

/*-
 * #%L
 * mastodon-deep-lineage
 * %%
 * Copyright (C) 2022 - 2025 Stefan Hahmann
 * %%
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 * modification, are permitted provided that the following conditions are met:
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 *    this list of conditions and the following disclaimer.
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package org.mastodon.mamut.detection.cellpose;

import java.io.IOException;

import javax.annotation.Nullable;

import org.apposed.appose.Service;
import org.mastodon.mamut.util.ResourceUtils;

/**
 * Cellpose3 is a specialized implementation of the {@link Cellpose} class, specifically
 * designed to use Cellpose version 4 model for cell segmentation tasks.<br>
 */
public class Cellpose4 extends Cellpose
{
	public static final String ENV_NAME = "cellpose4";

	public static final String ENV_FILE_CONTENT =
			ResourceUtils.readResourceAsString( "org/mastodon/mamut/detection/cellpose/cellpose4.toml", Cellpose4.class )
					.replace( "{ENV_NAME}", ENV_NAME )
					.replace( "{APPOSE_VERSION}", APPOSE_PYTHON_VERSION );

	public Cellpose4( final Service python, final @Nullable org.scijava.log.Logger scijavaLogger ) throws IOException
	{
		super( python, scijavaLogger );
	}

	@Override
	protected String getLoadModelCommand()
	{
		return "model = models.CellposeModel(gpu=torch.cuda.is_available())" + "\n";
	}

	@Override
	protected String getEvaluateModelCommand()
	{
		String zAxis = is3D() ? "0" : "None";
		return "segmentation, flows, styles = model.eval("
				+ "image_ndarray, "
				+ "diameter=" + getDiameter() + ", "
				+ "do_3D=" + is3DParam() + ", "
				+ "z_axis=" + zAxis + ", "
				+ "normalize=True, "
				+ "batch_size=8, "
				+ "flow3D_smooth=0, "
				+ "flow_threshold=" + flowThreshold + ", "
				+ "cellprob_threshold=" + cellProbThreshold + ")" + "\n";
	}
}