Draft: Plugin classes

Classes for the ImageJ plugin.

src/main/java/StartingOSStats.java

+
+import ij.ImageJ;
+import io.scif.img.IO;
+import io.scif.img.SCIFIOImgPlus;
+import net.imglib2.img.Img;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.TreeMap;
+
+public class StartingOSStats
+{
+
+    BufferedWriter writer;
+    FileWriter fileWriter;
+    private final String path =  "C:\\Users\\ctrebeau\\Desktop\\stats\\";
+
+    public StartingOSStats( String fileName  ) throws IOException
+    {
+        fileName.replace( "tif", "txt" );
+        writer = new BufferedWriter(new FileWriter(fileName));
+        writer.write(path + fileName  );
+    }
+
+
+    public void writeParameter(String amplitude, String otsu, String sigmas, String delta) throws IOException
+    {
+        StringBuilder s = new StringBuilder(
+                "Amplitude percent : " + amplitude +
+                "Otsu percent : " +otsu + System.lineSeparator() +
+                "Sigmas : " + sigmas + System.lineSeparator()+
+                "Delta : " + delta + System.lineSeparator());
+
+        writer.write( s.toString() );
+    }
+
+    public void close() throws IOException
+    {
+        writer.close();
+    }
+
+    public void writeHistogram(  TreeMap<Integer, Integer> map ) throws IOException
+    {
+        writer.write(map.toString());
+    }
+
+    public void writeInfo( String info, double value) throws IOException
+    {
+        writer.write( info + " : " + value );
+    }
+    public static < T extends RealType< T > & NativeType< T > > void main( String[] args ) throws IOException
+    {
+        String path = "C:\\Users\\ctrebeau\\Desktop\\MoucheAile\\STK\\";
+        String fileName = "STK_Mouche_c01_f0001_p005.tif";
+
+        // Input of the image.
+        final String imagePath = path + fileName;
+//        "doc/BG2.tif";
+
+
+
+
+        System.out.println("File : " + fileName );
+
+
+        ImageJ ij = new ImageJ();
+        /* JY version for opening files. */
+        final SCIFIOImgPlus< ? > imgPlus = IO.openImgs( imagePath ).get( 0 );
+
+        final Img< T > stackImage = ( Img < T > ) imgPlus.getImg();
+
+
+        /* User Parameters AKA arguments to run the program*/
+        double amplitude = Double.parseDouble( args[ 0 ] );
+        double otsu = Double.parseDouble( args[ 1 ] );
+        int sigmas = Integer.parseInt( args[ 2 ] );
+        int k1 = Integer.parseInt( args[ 3 ] );
+        double percent1 = Double.parseDouble( args[ 4 ] );
+        int k2 = Integer.parseInt( args[ 5 ] );
+        double percent2 = Double.parseDouble( args[ 6 ] );
+        int delta = Integer.parseInt( args[ 7 ] );
+        /* End of parameters. */
+
+//        UserParameters userParameters = new UserParameters( amplitude, otsu, sigmas, delta, "MIP", 0 );
+//        AdvancedUserParameters advancedUserParameters = new AdvancedUserParameters( k1, percent1, k2, percent2 );
+//
+//        IJ.log("Type: "+ imgPlus.firstElement().getClass().toGenericString());
+//
+//        if ( stackImage.numDimensions() == 3 )// Is it a stack ?
+//        {
+////            ImageJFunctions.show( stackImage, "original" );
+////            ImageJFunctions.show( TestMIP.findMIP( stackImage, stackImage.factory() ), "MIP" );
+//            new ReferenceSurfaceExtraction<>( stackImage, stackImage.factory(),userParameters, advancedUserParameters );
+//        }
+//        else
+//        {
+//            System.out.println( " This image has to be a z-stack ! " );
+//        }
+//        StartingOSStats startingOSStats = new StartingOSStats( fileName );
+//        startingOSStats.writeParameter( args[ 0 ] , args[ 1 ] , args[ 2 ], args[ 3 ]  );
+//        startingOSStats.writeInfo( "OS count ", OSE.getCount() );
+////        startingOSStats.writeHistogram( OSE.getOcc() );
+//        startingOSStats.close();
+    }
+}