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Commits (9)
Branches (with "parent <- child" branch notation):
developJava6 <- masterJava6 <- java16
are kept for possibility to build and deliver MosaicSuite compatibile with old ImageJ1 and Fiji based on Java6.
They are not used for current development which is kept on develop <- master branches.
Original purpose was:
developJava6 - development branch (new features and fixes)
masterJava6 - stable branch - things to be released (tests here still require Java7)
java16 - actuall release branch with some changes (like removed tests) that allows to build it with java6
ImageJ
build
clean
compress
main
File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters: background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;3;25.3333;48.0;1.3333
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
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0;0;21.0;41.0;2.0;2130.03187090407;14.523809432983398;10.904762268066406;1.1904761791229248
0;0;35.0;55.0;0.0;1019.5706596908651;0.6000000238418579;12.571428298950195;10.742856979370117
0;0;20.0;48.0;2.0;5658.4965660007965;9.800000190734863;17.799999237060547;14.800000190734863
File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters:background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;3;25.3333;48.0;1.3333
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602330370/tmp_1.tif
0;0;21.0;41.0;2.0;2130.03187090407;14.523809432983398;10.904762268066406;1.1904761791229248
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0;0;20.0;48.0;2.0;5658.4965660007965;9.800000190734863;17.799999237060547;14.800000190734863
File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters: background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;4;5.25;16.0;1.75
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602335480/tmp_1.tif
0;0;7.0;26.0;2.0;4195.096491167105;16.285715103149414;7.285714149475098;3.7142856121063232
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0;0;3.0;7.0;1.0;522.4448319627804;6.333333492279053;0.3333333432674408;14.0
0;0;4.0;18.0;1.0;17512.42638264492;11.25;15.25;14.25
File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters:background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;4;5.25;16.0;1.75
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602335480/tmp_1.tif
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0;0;3.0;7.0;1.0;522.4448319627804;6.333333492279053;0.3333333432674408;14.0
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File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters: background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;2;27.0;54.5;2.0
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602339577/tmp_1.tif
0;0;29.0;66.0;2.0;1800.1588839831986;17.79310417175293;7.896551609039307;5.482758522033691
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File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters:background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;2;27.0;54.5;2.0
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602339577/tmp_1.tif
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0;0;25.0;43.0;2.0;1317.6769026725592;0.5600000023841858;6.800000190734863;11.720000267028809
File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters: background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;2;44.5;90.0;2.0
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602344538/tmp_1.tif
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File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters:background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;2;44.5;90.0;2.0
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602344538/tmp_1.tif
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0;0;25.0;58.0;2.0;4065.83182541896;7.800000190734863;14.720000267028809;13.4399995803833
File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters: background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;2;16.5;48.0;1.5
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602349301/tmp_1.tif
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File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters:background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;2;16.5;48.0;1.5
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602349301/tmp_1.tif
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File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
%Parameters: background removal false window size 10 stddev PSF xy 1.5 stddev PSF z 3.44 Regularization 0.2 0.2 Min intensity ch1 0.1 Min intensity ch2 0.1 subpixel false Cell mask ch1 false mask threshold ch1 0.0015 Cell mask ch2 false mask threshold ch2 0.0015 Intensity estimation Automatic Noise model Poisson;
tmp_1.tif;0;2;21.5;61.0;3.0
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602353909/tmp_1.tif
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File;Image ID;Objects ch1;Mean size in ch1;Mean surface in ch1;Mean length in ch1
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tmp_1.tif;0;2;21.5;61.0;3.0
Image_ID;Object_ID;Size;Perimeter;Length;Intensity;Coord_X;Coord_Y;Coord_Z
%background:/home/gonciarz/scratch/session1457602353909/tmp_1.tif
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FileName;Frame;Channel;NumOfObjects;MeanSize;MeanSurface;MeanLength
%background:/home/gonciarz/scratch/session1457602330370/tmp_1.tif
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tmp_1.tif;0;0;3;25.3333;48.0;1.3333
FileName;Frame;Channel;Id;X;Y;Z;Size;Perimeter;Length;Intensity
%background:/home/gonciarz/scratch/session1457602330370/tmp_1.tif
tmp_1.tif;0;0;1;14.523809432983398;10.904762268066406;1.1904761791229248;21.0;41.0;2.0;2130.03187090407
%background:/home/gonciarz/scratch/session1474886218064/tmp_1.tif
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tmp_1.tif;0;0;2;0.6000000238418579;12.571428298950195;10.742856979370117;35.0;55.0;0.0;1019.5706596908651
tmp_1.tif;0;0;3;9.800000190734863;17.799999237060547;14.800000190734863;20.0;48.0;2.0;5658.4965660007965
FileName;Frame;Channel;NumOfObjects;MeanSize;MeanSurface;MeanLength
%background:/home/gonciarz/scratch/session1457602330370/tmp_1.tif
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FileName;Frame;Channel;Id;X;Y;Z;Size;Perimeter;Length;Intensity
%background:/home/gonciarz/scratch/session1457602330370/tmp_1.tif
tmp_1.tif;0;0;1;14.523809432983398;10.904762268066406;1.1904761791229248;21.0;41.0;2.0;2130.03187090407
%background:/home/gonciarz/scratch/session1474886218064/tmp_1.tif
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tmp_1.tif;0;0;3;9.800000190734863;17.799999237060547;14.800000190734863;20.0;48.0;2.0;5658.4965660007965
FileName;Frame;Channel;NumOfObjects;MeanSize;MeanSurface;MeanLength
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FileName;Frame;Channel;Id;X;Y;Z;Size;Perimeter;Length;Intensity
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tmp_1.tif;0;0;3;6.333333492279053;0.3333333432674408;14.0;3.0;7.0;1.0;522.4448319627804
......
FileName;Frame;Channel;NumOfObjects;MeanSize;MeanSurface;MeanLength
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......
FileName;Frame;Channel;NumOfObjects;MeanSize;MeanSurface;MeanLength
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FileName;Frame;Channel;Id;X;Y;Z;Size;Perimeter;Length;Intensity
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FileName;Frame;Channel;NumOfObjects;MeanSize;MeanSurface;MeanLength
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FileName;Frame;Channel;NumOfObjects;MeanSize;MeanSurface;MeanLength
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FileName;Frame;Channel;NumOfObjects;MeanSize;MeanSurface;MeanLength
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%background:/home/gonciarz/scratch/session1474886230537/tmp_1.tif
tmp_1.tif;0;0;2;21.5;61.0;3.0
FileName;Frame;Channel;Id;X;Y;Z;Size;Perimeter;Length;Intensity
%background:/home/gonciarz/scratch/session1457602353909/tmp_1.tif
%background:/home/gonciarz/scratch/session1474886230537/tmp_1.tif
tmp_1.tif;0;0;1;19.19230842590332;14.615385055541992;3.423076868057251;26.0;70.0;3.0;1787.5943960874624
tmp_1.tif;0;0;2;11.176470756530762;15.823529243469238;14.0;17.0;52.0;3.0;5401.7056180885
tmp_1.tif;0;0;2;11.176470756530762;15.823529243469238;14.0;17.0;52.0;3.0;5401.705618088499
......@@ -23,27 +23,7 @@
<property name="name" value="Mosaic" />
<property name="jarfilename" value="Mosaic_ToolSuite" />
<target name="jtest" depends="buildTest">
<junit printsummary="yes" haltonfailure="yes">
<classpath>
<pathelement location="bin" />
<fileset dir="lib">
<include name="*.jar" />
</fileset>
<fileset dir="lib/bio-formats">
<include name="*.jar" />
</fileset>
</classpath>
<batchtest>
<fileset dir="${test}">
<include name="**/*Test*" />
</fileset>
</batchtest>
<formatter type="brief" usefile="false"/>
</junit>
</target>
<target name="main" depends="clean,build,compress,buildTest" description="Main target">
<target name="main" depends="clean,build,compress" description="Main target">
<echo>
Clean, compile and compressing the .jar file.
......@@ -51,7 +31,7 @@
</echo>
</target>
<target name="ImageJ" depends="" description="Generate the distribution">
<target name="ImageJ" depends="clean,build,compress" description="Generate the distribution">
<echo>
Building the .jar file.
</echo>
......@@ -88,7 +68,7 @@
<zipfileset src="lib/commons-beanutils-1.8.3.jar" excludes="META-INF/**" />
<zipfileset src="lib/commons-lang3-3.1.jar" excludes="META-INF/**" />
<zipfileset src="lib/commons-logging-1.1.3.jar" excludes="META-INF/**" />
<zipfileset src="lib/dozer-5.4.0.jar" excludes="META-INF/**" />
<zipfileset src="lib/dozer-5.5.1.jar" excludes="META-INF/**" />
<zipgroupfileset dir="lib" includes="javaml-0.1.7.jar" excludes="*.config" />
<zipfileset src="lib/jtransforms-2.4.jar" excludes="META-INF/**" />
<zipgroupfileset dir="lib" includes="mines-jtk-20100113.jar" excludes="*.config" />
......@@ -145,17 +125,5 @@
<compilerarg line="-Xmaxwarns 10000" />
</javac>
</target>
<target name="buildTest" depends="build">
<mkdir dir="${build}" />
<javac debug="true" includeantruntime="false" srcdir="test/" destdir="bin/" classpathref="build.classpath" classpath="${build.classpath}" source="1.7" target="1.7">
<compilerarg value="-Xlint:all" />
<compilerarg value="-Xlint:-path" />
<compilerarg value="-proc:none" />
<compilerarg value="-Xlint:-options"/>
<compilerarg value="-Werror" />
<compilerarg line="-Xmaxwarns 10000" />
</javac>
</target>
</project>
......@@ -41,7 +41,7 @@ class PSFWindow implements ActionListener, PropertyChangeListener {
private final JFormattedTextField Vpix_xy = new JFormattedTextField(nf);
private final JFormattedTextField Vpix_z = new JFormattedTextField(nf);
private final JComboBox<String> micr = new JComboBox<String>(items);
private final JComboBox micr = new JComboBox(items);
private final JButton estimate = new JButton("Compute PSF");
private final JLabel ref = new JLabel("<html>" + "<div align=\"justify\">" + "Gaussian PSF approximation." + "<br>" + "<br>"
......
......@@ -89,7 +89,7 @@ public class ClusterGUI extends JDialog {
//
final JComboBox<String> comboBox_1 = new JComboBox<String>(CBcp);
final JComboBox comboBox_1 = new JComboBox(CBcp);
comboBox_1.setSelectedIndex(cp.length - 1);
comboBox_1.addActionListener(new ActionListener() {
......
......@@ -37,7 +37,7 @@ abstract public class InteractionAnalysisGuiBase implements ActionListener {
protected JFormattedTextField kernelWeightQ;
protected JFormattedTextField kernelWeightP;
protected JButton calculateDistances;
protected JComboBox<String> potentialComboBox;
protected JComboBox potentialComboBox;
protected JFormattedTextField reRuns;
protected JLabel numOfsupportPointsLabel, smoothnessLabel;
protected JFormattedTextField numOfSupportPoints, smoothness;
......@@ -137,7 +137,7 @@ abstract public class InteractionAnalysisGuiBase implements ActionListener {
final JLabel lblPotentialEstimation = new JLabel("Potential estimation");
potentialComboBox = new JComboBox<String>(potentials);
potentialComboBox = new JComboBox(potentials);
potentialComboBox.setSelectedIndex(1);
potentialComboBox.addActionListener(this);
......
......@@ -10,7 +10,7 @@ import net.imglib2.img.ImagePlusAdapter;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
public class ColorSubstitution implements ExtendedPlugInFilter // NO_UCD
{
......@@ -50,7 +50,7 @@ public class ColorSubstitution implements ExtendedPlugInFilter // NO_UCD
final double col_from = gd.getNextNumber();
final double col_to = gd.getNextNumber();
substitute(imp,col_from,col_to);
this.<UnsignedByteType> substitute(imp,col_from,col_to);
return DONE;
}
......
......@@ -151,7 +151,7 @@ public class Naturalization extends PlugIn8bitBase
final float Nf = findNaturalizationFactor(image_orig, Theta, T2_prior);
result[0] = Nf;
final Img<T> image_result = naturalizeImage(image_orig, Nf, cls_t);
final Img<T> image_result = this.<S,T> naturalizeImage(image_orig, Nf, cls_t);
return image_result;
}
......
......@@ -153,10 +153,10 @@ public class Poisson_Noise implements ExtendedPlugInFilter {
final Object test_o = test;
if (test_o instanceof UnsignedByteType) {
return (BinMapper1d<T>) this.<UnsignedByteType>createIntegerMapper(256);
return (BinMapper1d<T>) (BinMapper1d<?>) this.<UnsignedByteType>createIntegerMapper(256);
}
else if (test_o instanceof ShortType) {
return (BinMapper1d<T>) this.<ShortType>createIntegerMapper(65536);
return (BinMapper1d<T>) (BinMapper1d<?>) this.<ShortType>createIntegerMapper(65536);
}
else if (test_o instanceof FloatType) {
return new Real1dBinMapper<T>(min,max,65536,true);
......
......@@ -53,7 +53,7 @@ public class RCWWin extends JDialog implements MouseListener, Runnable {
protected Settings ref_save;
private final JPanel contentPane;
private final JComboBox<String> b1;
private final JComboBox b1;
private ImagePlus img[];
protected segType sT;
......@@ -133,7 +133,7 @@ public class RCWWin extends JDialog implements MouseListener, Runnable {
contentPane.add(lblNewLabel);
sT = segType.Tissue;
final JComboBox<segType> comboBox = new JComboBox<segType>(segType.values());
final JComboBox comboBox = new JComboBox(segType.values());
contentPane.add(comboBox);
comboBox.addActionListener(new ActionListener() {
......@@ -152,13 +152,13 @@ public class RCWWin extends JDialog implements MouseListener, Runnable {
final JLabel lblNewLabel_2 = new JLabel("<html>Select a region of interest <br>with the imageJ selection<br> tool</html>");
contentPane.add(lblNewLabel_2);
final JComboBox<String> comboBox_1 = new JComboBox<String>();
final JComboBox comboBox_1 = new JComboBox();
final String[] md = GetROI();
comboBox_1.setBackground(Color.YELLOW);
contentPane.add(comboBox_1);
comboBox_1.setModel((new DefaultComboBoxModel<String>(md)));
comboBox_1.setModel((new DefaultComboBoxModel(md)));
b1 = comboBox_1;
......@@ -225,7 +225,7 @@ public class RCWWin extends JDialog implements MouseListener, Runnable {
@Override
public void mousePressed(MouseEvent arg0) {
final String[] md = GetROI();
b1.setModel((new DefaultComboBoxModel<String>(md)));
b1.setModel((new DefaultComboBoxModel(md)));
}
@Override
......