1 package com.github.celldynamics.quimp.filesystem;
2
3 import java.util.ArrayList;
4
5 import org.slf4j.Logger;
6 import org.slf4j.LoggerFactory;
7
8 import com.github.celldynamics.quimp.OutlineHandler;
9
10 /**
11 * Represent collection of OutlineHandlers for cells.
12 *
13 * <p>This class is used as storage of OutlineHandlers (results of continuous segmentation) in
14 * {@link com.github.celldynamics.quimp.filesystem.DataContainer}.
15 *
16 * @author p.baniukiewicz
17 *
18 */
19 public class OutlinesCollection implements IQuimpSerialize {
20
21 /**
22 * The Constant LOGGER.
23 */
24 static final Logger LOGGER = LoggerFactory.getLogger(OutlinesCollection.class.getName());
25 /**
26 * Contain {@link OutlineHandler} objects.
27 *
28 * <p>Each object ({@link OutlineHandler} represents segmented cell (outline) between frame
29 * <it>f1</it> and <it>f2</it> but only if segmentation process run continuously between these
30 * frames. Outlines are returned by of ECMM module and they are almost the same as Snakes but
31 * may differ in node order or number.
32 *
33 */
34 public ArrayList<OutlineHandler> oHs;
35
36 /**
37 * Instantiates a new outlines collection.
38 *
39 * @param size the size
40 */
41 public OutlinesCollection(int size) {
42 oHs = new ArrayList<>(size);
43 }
44
45 /**
46 * Instantiates a new outlines collection.
47 */
48 public OutlinesCollection() {
49 oHs = new ArrayList<>();
50 }
51
52 /**
53 * Prepare Outlines for serialization. Build arrays from Outline objects stored in
54 * OutlineHandlers
55 */
56 @Override
57 public void beforeSerialize() {
58 if (oHs != null) {
59 for (OutlineHandler oh : oHs) {
60 oh.beforeSerialize();
61 }
62 }
63 }
64
65 /**
66 * Rebuild every Outline from temporary array.
67 */
68 @Override
69 public void afterSerialize() throws Exception {
70 if (oHs != null) {
71 for (OutlineHandler oh : oHs) {
72 oh.afterSerialize();
73 }
74 }
75 }
76 }