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tineveztinevez
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Merge pull request #3 from trackmate-sc/v8-new
Acquaint to the new TrackMate v8 API
2 parents 4ad9501 + f18b5b2 commit 77ee678

4 files changed

Lines changed: 27 additions & 127 deletions

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‎pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -5,13 +5,13 @@
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<parent>
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<groupId>org.scijava</groupId>
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<artifactId>pom-scijava</artifactId>
8-
<version>37.0.0</version>
8+
<version>43.0.0</version>
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<relativePath />
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</parent>
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<groupId>sc.fiji</groupId>
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<artifactId>TrackMate-MorphoLibJ</artifactId>
14-
<version>1.2.2-SNAPSHOT</version>
14+
<version>2.0.0-SNAPSHOT</version>
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<name>TrackMate-MorphoLibJ</name>
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<description>TrackMate detector based on the watershed segmentation tool in the MorphoLibJ plugin.</description>
@@ -84,7 +84,7 @@
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<!-- NB: Deploy releases to the SciJava Maven repository. -->
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<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
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87-
<TrackMate.version>7.10.2</TrackMate.version>
87+
<TrackMate.version>8.0.0</TrackMate.version>
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</properties>
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<dependencies>

‎src/main/java/fiji/plugin/trackmate/morpholibj/MorphoLibJDetectorConfigurationPanel.java‎

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@@ -8,12 +8,12 @@
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* it under the terms of the GNU General Public License as
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* published by the Free Software Foundation, either version 3 of the
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* License, or (at your option) any later version.
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*
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
16+
*
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* You should have received a copy of the GNU General Public
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* License along with this program. If not, see
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* <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -25,6 +25,7 @@
2525
import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SIMPLIFY_CONTOURS;
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import static fiji.plugin.trackmate.gui.Fonts.BIG_FONT;
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import static fiji.plugin.trackmate.gui.Fonts.SMALL_FONT;
28+
import static fiji.plugin.trackmate.morpholibj.MorphoLibJDetectorFactory.ICON;
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import static fiji.plugin.trackmate.morpholibj.MorphoLibJDetectorFactory.KEY_CONNECTIVITY;
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import static fiji.plugin.trackmate.morpholibj.MorphoLibJDetectorFactory.KEY_TOLERANCE;
3031

@@ -33,15 +34,13 @@
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import java.awt.GridBagConstraints;
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import java.awt.GridBagLayout;
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import java.awt.Insets;
36-
import java.net.URL;
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import java.text.DecimalFormat;
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import java.text.NumberFormat;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.Vector;
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44-
import javax.swing.ImageIcon;
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import javax.swing.JCheckBox;
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import javax.swing.JComboBox;
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import javax.swing.JFormattedTextField;
@@ -64,8 +63,6 @@ public class MorphoLibJDetectorConfigurationPanel extends ConfigurationPanel
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private static final NumberFormat THRESHOLD_FORMAT = new DecimalFormat( "#.##" );
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67-
protected static final ImageIcon ICON = new ImageIcon( getResource( "images/TrackMateMorphoLibJ-logo-100px.png" ) );
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private static final String TITLE = MorphoLibJDetectorFactory.NAME;
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private final JSlider sliderChannel;
@@ -80,9 +77,8 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
8077
{
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final GridBagLayout gridBagLayout = new GridBagLayout();
8279
gridBagLayout.columnWidths = new int[] { 144, 0, 32 };
83-
gridBagLayout.rowHeights = new int[] { 0, 84, 0, 27, 0, 0, 0 };
80+
gridBagLayout.rowHeights = new int[] { 0, 84, 0, 27, 0, 0, 150 };
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gridBagLayout.columnWeights = new double[] { 0.0, 1.0, 0.0 };
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gridBagLayout.rowWeights = new double[] { 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
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setLayout( gridBagLayout );
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final JLabel lblDetector = new JLabel( TITLE, ICON, JLabel.RIGHT );
@@ -107,7 +103,14 @@ public MorphoLibJDetectorConfigurationPanel( final Settings settings, final Mode
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gbcLblHelptext.insets = new Insets( 5, 5, 5, 5 );
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gbcLblHelptext.gridx = 0;
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gbcLblHelptext.gridy = 1;
110-
add( GuiUtils.textInScrollPanel( GuiUtils.infoDisplay( MorphoLibJDetectorFactory.INFO_TEXT ) ), gbcLblHelptext );
106+
gbcLblHelptext.weighty = 1.;
107+
add( GuiUtils.textInScrollPanel( GuiUtils.infoDisplay(
108+
MorphoLibJDetectorFactory.INFO_TEXT.replace( "</html>", "" )
109+
+ "<html>Online documentation: <br/>"
110+
+ "<a href='" + MorphoLibJDetectorFactory.DOC_URL + "'>"
111+
+ MorphoLibJDetectorFactory.DOC_URL
112+
+ "</a></html>" ) ),
113+
gbcLblHelptext );
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/*
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* Channel selector.
@@ -301,9 +304,4 @@ public void setSettings( final Map< String, Object > settings )
301304
@Override
302305
public void clean()
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{}
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protected static URL getResource( final String name )
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{
307-
return MorphoLibJDetectorFactory.class.getClassLoader().getResource( name );
308-
}
309307
}

‎src/main/java/fiji/plugin/trackmate/morpholibj/MorphoLibJDetectorFactory.java‎

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Original file line numberDiff line numberDiff line change
@@ -8,12 +8,12 @@
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* it under the terms of the GNU General Public License as
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* published by the Free Software Foundation, either version 3 of the
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* License, or (at your option) any later version.
11-
*
11+
*
1212
* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
1414
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
1515
* GNU General Public License for more details.
16-
*
16+
*
1717
* You should have received a copy of the GNU General Public
1818
* License along with this program. If not, see
1919
* <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -24,29 +24,20 @@
2424
import static fiji.plugin.trackmate.detection.DetectorKeys.DEFAULT_TARGET_CHANNEL;
2525
import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL;
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import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SIMPLIFY_CONTOURS;
27-
import static fiji.plugin.trackmate.io.IOUtils.readBooleanAttribute;
28-
import static fiji.plugin.trackmate.io.IOUtils.readDoubleAttribute;
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import static fiji.plugin.trackmate.io.IOUtils.readIntegerAttribute;
30-
import static fiji.plugin.trackmate.io.IOUtils.writeAttribute;
31-
import static fiji.plugin.trackmate.io.IOUtils.writeTargetChannel;
32-
import static fiji.plugin.trackmate.util.TMUtils.checkMapKeys;
33-
import static fiji.plugin.trackmate.util.TMUtils.checkParameter;
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35-
import java.util.ArrayList;
3628
import java.util.HashMap;
37-
import java.util.List;
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import java.util.Map;
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4031
import javax.swing.ImageIcon;
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42-
import org.jdom2.Element;
4333
import org.scijava.Priority;
4434
import org.scijava.plugin.Plugin;
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4636
import fiji.plugin.trackmate.Model;
4737
import fiji.plugin.trackmate.Settings;
4838
import fiji.plugin.trackmate.detection.SpotDetector;
4939
import fiji.plugin.trackmate.detection.SpotDetectorFactory;
40+
import fiji.plugin.trackmate.gui.GuiUtils;
5041
import fiji.plugin.trackmate.gui.components.ConfigurationPanel;
5142
import fiji.plugin.trackmate.util.TMUtils;
5243
import net.imagej.ImgPlus;
@@ -57,11 +48,6 @@
5748
@Plugin( type = SpotDetectorFactory.class, priority = Priority.LOW - 5. )
5849
public class MorphoLibJDetectorFactory< T extends RealType< T > & NativeType< T > > implements SpotDetectorFactory< T >
5950
{
60-
61-
/*
62-
* CONSTANTS
63-
*/
64-
6551
/**
6652
* The key to the parameter that stores the tolerance value to use in
6753
* morphological segmentation. Accepted values are doubles.
@@ -99,29 +85,14 @@ public class MorphoLibJDetectorFactory< T extends RealType< T > & NativeType< T
9985
+ "also cite the MorphoLibJ paper: <a href=\"https://doi.org/10.1093/bioinformatics/btw413\">Legland, D.; Arganda-Carreras, I. & Andrey, P. (2016), "
10086
+ "'MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ', "
10187
+ "Bioinformatics (Oxford Univ Press) 32(22): 3532-3534.</a> "
102-
+ "<p>"
103-
+ "Documentation for this module "
104-
+ "<a href=\"https://imagej.net/plugins/trackmate/trackmate-morpholibj\">on the ImageJ Wiki</a>."
105-
+ "<p>"
10688
+ "</html>";
10789

108-
/*
109-
* FIELDS
110-
*/
111-
112-
/** The image to operate on. Multiple frames, single channel. */
113-
protected ImgPlus< T > img;
114-
115-
protected Map< String, Object > settings;
90+
public static final String DOC_URL = "https://imagej.net/plugins/trackmate/trackmate-morpholibj";
11691

117-
protected String errorMessage;
118-
119-
/*
120-
* METHODS
121-
*/
92+
public static final ImageIcon ICON = new ImageIcon( GuiUtils.getResource( "images/TrackMateMorphoLibJ-logo-64px.png", MorphoLibJDetectorFactory.class ) );
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12394
@Override
124-
public SpotDetector< T > getDetector( final Interval interval, final int frame )
95+
public SpotDetector< T > getDetector( final ImgPlus< T > img, final Map< String, Object > settings, final Interval interval, final int frame )
12596
{
12697
final int channel = ( Integer ) settings.get( KEY_TARGET_CHANNEL ) - 1;
12798
final ImgPlus< T > input = TMUtils.hyperSlice( img, channel, frame );
@@ -138,54 +109,6 @@ public SpotDetector< T > getDetector( final Interval interval, final int frame )
138109
return detector;
139110
}
140111

141-
@Override
142-
public boolean setTarget( final ImgPlus< T > img, final Map< String, Object > settings )
143-
{
144-
this.img = img;
145-
this.settings = settings;
146-
return checkSettings( settings );
147-
}
148-
149-
@Override
150-
public String getErrorMessage()
151-
{
152-
return errorMessage;
153-
}
154-
155-
@Override
156-
public boolean marshall( final Map< String, Object > settings, final Element element )
157-
{
158-
final StringBuilder errorHolder = new StringBuilder();
159-
boolean ok = writeTargetChannel( settings, element, errorHolder );
160-
ok = ok && writeAttribute( settings, element, KEY_TOLERANCE, Double.class, errorHolder );
161-
ok = ok && writeAttribute( settings, element, KEY_CONNECTIVITY, Integer.class, errorHolder );
162-
ok = ok && writeAttribute( settings, element, KEY_SIMPLIFY_CONTOURS, Boolean.class, errorHolder );
163-
164-
if ( !ok )
165-
errorMessage = errorHolder.toString();
166-
167-
return ok;
168-
}
169-
170-
@Override
171-
public boolean unmarshall( final Element element, final Map< String, Object > settings )
172-
{
173-
settings.clear();
174-
final StringBuilder errorHolder = new StringBuilder();
175-
boolean ok = true;
176-
ok = ok && readIntegerAttribute( element, settings, KEY_TARGET_CHANNEL, errorHolder );
177-
ok = ok && readDoubleAttribute( element, settings, KEY_TOLERANCE, errorHolder );
178-
ok = ok && readIntegerAttribute( element, settings, KEY_CONNECTIVITY, errorHolder );
179-
ok = ok && readBooleanAttribute( element, settings, KEY_SIMPLIFY_CONTOURS, errorHolder );
180-
181-
if ( !ok )
182-
{
183-
errorMessage = errorHolder.toString();
184-
return false;
185-
}
186-
return checkSettings( settings );
187-
}
188-
189112
@Override
190113
public ConfigurationPanel getDetectorConfigurationPanel( final Settings settings, final Model model )
191114
{
@@ -204,36 +127,21 @@ public Map< String, Object > getDefaultSettings()
204127
}
205128

206129
@Override
207-
public boolean checkSettings( final Map< String, Object > settings )
130+
public String getInfoText()
208131
{
209-
boolean ok = true;
210-
final StringBuilder errorHolder = new StringBuilder();
211-
ok = ok & checkParameter( settings, KEY_TARGET_CHANNEL, Integer.class, errorHolder );
212-
ok = ok & checkParameter( settings, KEY_TOLERANCE, Double.class, errorHolder );
213-
ok = ok & checkParameter( settings, KEY_CONNECTIVITY, Integer.class, errorHolder );
214-
ok = ok & checkParameter( settings, KEY_SIMPLIFY_CONTOURS, Boolean.class, errorHolder );
215-
final List< String > mandatoryKeys = new ArrayList<>();
216-
mandatoryKeys.add( KEY_TARGET_CHANNEL );
217-
mandatoryKeys.add( KEY_TOLERANCE );
218-
mandatoryKeys.add( KEY_CONNECTIVITY );
219-
mandatoryKeys.add( KEY_SIMPLIFY_CONTOURS );
220-
ok = ok & checkMapKeys( settings, mandatoryKeys, null, errorHolder );
221-
if ( !ok )
222-
errorMessage = errorHolder.toString();
223-
224-
return ok;
132+
return INFO_TEXT;
225133
}
226134

227135
@Override
228-
public String getInfoText()
136+
public ImageIcon getIcon()
229137
{
230-
return INFO_TEXT;
138+
return ICON;
231139
}
232140

233141
@Override
234-
public ImageIcon getIcon()
142+
public String getUrl()
235143
{
236-
return null;
144+
return DOC_URL;
237145
}
238146

239147
@Override
@@ -253,10 +161,4 @@ public boolean has2Dsegmentation()
253161
{
254162
return true;
255163
}
256-
257-
@Override
258-
public MorphoLibJDetectorFactory< T > copy()
259-
{
260-
return new MorphoLibJDetectorFactory<>();
261-
}
262164
}

‎src/main/resources/images/TrackMateMorphoLibJ-logo-64px.png‎

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