1 package com.github.celldynamics.quimp.plugin.protanalysis;
2
3 import java.awt.Polygon;
4 import java.awt.geom.Point2D;
5 import java.util.Collection;
6
7 import org.apache.commons.lang3.NotImplementedException;
8 import org.scijava.vecmath.Point2d;
9 import org.slf4j.Logger;
10 import org.slf4j.LoggerFactory;
11
12 import com.github.celldynamics.quimp.plugin.qanalysis.STmap;
13
14 import ij.plugin.filter.MaximumFinder;
15 import ij.process.ByteProcessor;
16 import ij.process.ImageProcessor;
17
18 /**
19 * Calculate maxima for image.
20 *
21 * <p>Support various methods of finding maxima in ImageJ image.
22 *
23 * @author p.baniukiewicz
24 *
25 */
26 public class MaximaFinder {
27
28 /**
29 * The Constant LOGGER.
30 */
31 static final Logger LOGGER = LoggerFactory.getLogger(MaximaFinder.class.getName());
32 private ImageProcessor ip;
33 private Polygon maxima; // found maxima as polygon
34
35 // /**
36 // * Indicate that image processor has been rotated. By default x coordinate should be frame, y
37 // * index. But For visualisation is better to rotate image to have longer axis on bottom.
38 // * By default TrackVisualisation.Map.Map(String, float[][]) rotates image.
39 // */
40 // public boolean ROTATED = true;
41
42 /**
43 * Construct MaximaFinder object.
44 *
45 * @param ip Image processor with image to analyse.
46 */
47 public MaximaFinder(ImageProcessor ip) {
48 this.ip = ip;
49 maxima = null;
50 }
51
52 /**
53 * Compute maxima using ImageJ procedure.
54 *
55 * @param tolerance tolerance
56 * @see <a href=
57 * "link">https://rsb.info.nih.gov/ij/developer/api/ij/plugin/filter/MaximumFinder.html</a>
58 */
59 public void computeMaximaIJ(double tolerance) {
60 MaximumFinder mf = new MaximumFinder();
61 // maxima = mf.getMaxima(ip, tolerance, false); // stopped working for 1.52n
62 ByteProcessor ret = mf.findMaxima(ip, tolerance, MaximumFinder.SINGLE_POINTS, false);
63 maxima = new Polygon();
64 for (int x = 0; x < ret.getWidth(); ++x) {
65 for (int y = 0; y < ret.getHeight(); ++y) {
66 if (ret.get(x, y) > 0) {
67 maxima.addPoint(x, y);
68 }
69 }
70 }
71 LOGGER.debug("Found maxima: " + maxima.npoints);
72 }
73
74 /**
75 * Compute maxima from image where points different from background stand for location of maxima
76 * in <tt>ip</tt>.
77 *
78 * <p>This method can be used for restoring maxima in compatible format supported by this class
79 * from other image created outside.
80 *
81 * @param mximaMap map of maxima in image used for constructing this object
82 */
83 public void computeMaximaImage(ImageProcessor mximaMap) {
84 // TODO finish computeMaximaImage method
85 throw new NotImplementedException("Not implemented");
86 }
87
88 /**
89 * Set maxima for this object.
90 *
91 * <p>This can be used for setting maxima explicitly. Any use of {@link #computeMaximaIJ(double)}
92 * or
93 * {@link #computeMaximaImage(ImageProcessor)} will override these values.
94 *
95 * @param maxi list of maxima coordinates.
96 */
97 public void setMaximad(Collection<Point2d> maxi) {
98 maxima = new Polygon();
99 for (Point2d p : maxi) {
100 maxima.addPoint((int) p.getX(), (int) p.getY());
101 }
102
103 }
104
105 /**
106 * Set maxima for this object.
107 *
108 * <p>This can be used for setting maxima explicitly. Any use of {@link #computeMaximaIJ(double)}
109 * or
110 * {@link #computeMaximaImage(ImageProcessor)} will override these values.
111 *
112 * @param maxi list of maxima coordinates. Note that these values should relate to image
113 * coordinates (integer row and column) even if axis labels are different. Both coordinates
114 * are used for indexing {@link STmap}.
115 */
116 public void setMaxima(Collection<? extends Point2D> maxi) {
117 maxima = new Polygon();
118 for (Point2D p : maxi) {
119 maxima.addPoint((int) p.getX(), (int) p.getY());
120 }
121 }
122
123 /**
124 * Return values corresponding to indexes returned by getMaxima.
125 *
126 * <p>Must be called after getMaxima.
127 *
128 * @return Maxima in order of indexes returned by getMaxima.
129 */
130 public double[] getMaxValues() {
131 if (maxima == null) {
132 return new double[0];
133 }
134 double[] ret = new double[maxima.npoints];
135 for (int i = 0; i < maxima.npoints; i++) {
136 ret[i] = ip.getf(maxima.xpoints[i], maxima.ypoints[i]);
137 }
138 return ret;
139 }
140
141 /**
142 * getMaxima.
143 *
144 * @return Return maxima found by {@link #computeMaximaIJ(double)}. The coordinates depend on
145 * orientation of input image. For typical application like analysis of motility map, x
146 * axis stands for frames and y-axis for outline indexes.
147 */
148 public Polygon getMaxima() {
149 if (maxima == null) {
150 return new Polygon();
151 }
152 return maxima;
153 }
154
155 /**
156 * Number of points found.
157 *
158 * @return Number of points found.
159 */
160 public int getMaximaNumber() {
161 if (maxima == null) {
162 return 0;
163 }
164 return maxima.npoints;
165 }
166 }