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Fluorescence lifetime analysis in SciJava Ops.
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/*-
 * #%L
 * Fluorescence lifetime analysis in SciJava Ops.
 * %%
 * Copyright (C) 2024 SciJava developers.
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 * 
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
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 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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package org.scijava.ops.flim.impl;

import flimlib.FLIMLib;
import net.imglib2.type.numeric.RealType;
import org.scijava.ops.flim.AbstractFitRAI;
import org.scijava.ops.flim.FitParams;
import org.scijava.ops.flim.FitResults;
import org.scijava.ops.flim.FitWorker;

public class PhasorFit {

	/**
	 * Fits a RAI
	 *
	 * @param 
	 * @implNote op names="flim.fitPhasor"
	 */
	public static class PhasorSingleFitRAI, K extends RealType>
		extends AbstractFitRAI
	{

		@Override
		public FitWorker createWorker(FitParams params, FitResults results) {
			return new PhasorFit.PhasorFitWorker<>(params, results);
		}
	}

	public static class PhasorFitWorker> extends
		AbstractSingleFitWorker
	{

		private static final int NPARAMOUT = 6;
		// Phasor's own buffers
		private final float[] z, u, v, tau, tauPhi, tauMod;

		public PhasorFitWorker(FitParams params, FitResults results) {
			super(params, results);
			z = new float[1];
			u = new float[1];
			v = new float[1];
			tauPhi = new float[1];
			tauMod = new float[1];
			tau = new float[1];
		}

		@Override
		protected void beforeFit() {
			for (int i = 0; i < paramBuffer.length; i++) {
				// no estimation (+Inf was set by RAHelper#loadData)
				// this value makes phasor explode
				if (paramBuffer[i] == Float.POSITIVE_INFINITY) {
					paramBuffer[i] = 0;
				}
			}
			super.beforeFit();
			// setup params
			z[0] = paramBuffer[0];
			u[0] = paramBuffer[1];
			v[0] = paramBuffer[2];
			tauPhi[0] = paramBuffer[3];
			tauMod[0] = paramBuffer[4];
			tau[0] = paramBuffer[5];
		}

		@Override
		protected void doFit() {
			final int retCode = FLIMLib.GCI_Phasor(params.xInc, transBuffer,
				adjFitStart, adjFitEnd, z, u, v, tauPhi, tauMod, tau, fittedBuffer,
				residualBuffer, chisqBuffer);

			switch (retCode) {
				case -1: // PHASOR_ERR_INVALID_DATA (data == null)
				case -2: // PHASOR_ERR_INVALID_WINDOW (nbins < 0)
					results.retCode = FitResults.RET_BAD_SETTING;
					break;

				default: // non-negative: iteration count
					results.retCode = retCode >= 0 ? FitResults.RET_OK
						: FitResults.RET_UNKNOWN;
					break;
			}
		}

		@Override
		protected void afterFit() {
			// and copies back
			paramBuffer[0] = z[0];
			paramBuffer[1] = u[0];
			paramBuffer[2] = v[0];
			paramBuffer[3] = tauPhi[0];
			paramBuffer[4] = tauMod[0];
			paramBuffer[5] = tau[0];
			super.afterFit();
		}

		@Override
		public int nParamOut() {
			return NPARAMOUT;
		}

		@Override
		protected AbstractSingleFitWorker duplicate(FitParams params,
			FitResults rslts)
		{
			return new PhasorFitWorker<>(params, rslts);
		}
	}
}