Unit tests for CellposeSAM

Author: gletort

src/test/java/fiji/plugin/appose/cellpose/TestCellPoseSAMAppose.java

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+package fiji.plugin.appose.cellpose;
+
+import org.junit.jupiter.api.Test;
+import fiji.plugin.appose.cellpose.cp4.Cellpose4Parameters;
+import ij.IJ;
+import ij.ImagePlus;
+import ij.plugin.ChannelSplitter;
+import ij.plugin.Duplicator;
+import ij.plugin.RGBStackMerge;
+import ij.process.ImageStatistics;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+
+
+public class TestCellPoseSAMAppose 
+{
+	
+	@Test
+	public void defaultRunCPSAM() throws Exception
+	{
+		try 
+		{
+			final ImagePlus imp = IJ.openImage( "http://imagej.net/images/blobs.gif" );
+			// Get all default parameters
+			final Cellpose4Parameters paramsCP4 = Cellpose4Parameters.builder()
+			.build();
+			// Run it
+			final ImagePlus[] outputCP4 = Cellpose.cellpose4( imp, paramsCP4 );
+			// Get the label image results
+			final ImagePlus labelsCP4 = outputCP4[ 0 ];
+			// Check the label image dimensions
+			assertEquals( labelsCP4.getWidth(), imp.getWidth(), "CP4, 2D image: labels image dimension (width) is uncorrect" );
+			assertEquals( labelsCP4.getHeight(), imp.getHeight(), "CP4, 2D image: labels image dimension (height) is uncorrect" );
+			
+			// Check the label image statistics if it looks like a successfull run
+			ImageStatistics stats = labelsCP4.getStatistics();
+			assertFalse( stats.max <= 0, "CP4: No labels were found in blob image, with default parameters" );
+			assertTrue( stats.max > 50, "CP4: Not enough labels were found in blob image, with default parameters" );
+		}
+		catch (Exception e)
+		{
+			throw e;
+		}
+	}
+	
+	// Test different input image dimensions
+	@Test
+	public void defaultRunCPSAM_Image2DMultiChannels() throws Exception
+	{
+		
+		try 
+		{
+			// 2D image with 3 channels
+			final ImagePlus impRGB = IJ.openImage( "https://imagej.net/images/FluorescentCells.jpg" );
+			// convert RGB to composite ImagePlus
+			ImagePlus[] channels = ChannelSplitter.split( impRGB );
+		    final ImagePlus imp = RGBStackMerge.mergeChannels(channels, false);
+			// Get all default parameters
+			final Cellpose4Parameters paramsCP4 = Cellpose4Parameters.builder()
+			.build();
+			// Run it
+			final ImagePlus[] outputCP4 = Cellpose.cellpose4( imp, paramsCP4 );
+			// Get the label image results
+			final ImagePlus labelsCP4 = outputCP4[ 0 ];
+			// Check the label image dimensions
+			assertEquals( imp.getWidth(), labelsCP4.getWidth(), "CP4, 2D image: labels image dimension (width) is uncorrect" );
+			assertEquals( imp.getHeight(), labelsCP4.getHeight(), "CP4, 2D image: labels image dimension (height) is uncorrect" );
+			
+			// Check the label image statistics if it looks like a successfull run
+			ImageStatistics stats = labelsCP4.getStatistics();
+			assertFalse( stats.max <= 0, "CP4: No labels were found in blob image, with default parameters" );
+			assertTrue( stats.max > 3, "CP4: Not enough labels were found in blob image, with default parameters" );
+		}
+		catch (Exception e)
+		{
+			throw e;
+		}
+	}
+	
+	@Test
+	public void defaultRunCPSAM_Image3DMultiChannels() throws Exception
+	{	
+		// New image
+		try 
+		{
+			// 4D image with channels, Z, time
+			final ImagePlus stack = IJ.openImage( "https://imagej.net/images/mitosis.tif" );
+			// Keep only one time point
+			ImagePlus imp = new Duplicator().run(
+				    stack,
+				    1, stack.getNChannels(),   
+				    1, stack.getNSlices(),      
+				    3, 3     
+				);
+			// Get all default parameters
+			final Cellpose4Parameters paramsCP4 = Cellpose4Parameters.builder()
+					.chan0(0)
+					.chan1(null)
+					.do3D( false )
+					.stitchThreshold( 0.1 )
+			.build();
+			// Run it
+			final ImagePlus[] outputCP4 = Cellpose.cellpose4( imp, paramsCP4 );
+			// Get the label image results
+			final ImagePlus labelsCP4 = outputCP4[ 0 ];
+			// Check the label image dimensions
+			assertEquals( imp.getWidth(), labelsCP4.getWidth(), "CP4, 3D+chan image: labels image dimension (width) is uncorrect" );
+			assertEquals( imp.getHeight(), labelsCP4.getHeight(), "CP4, 3D+chanD image: labels image dimension (height) is uncorrect" );
+			
+			// Check the label image statistics if it looks like a successfull run
+			ImageStatistics stats = labelsCP4.getStatistics();
+			assertFalse( stats.max <= 0, "CP4: No labels were found in 4D image, with default parameters" );
+			assertTrue( stats.max == 1, "CP4: Too much labels were found in 4D image, with default parameters" );
+		}
+		catch (Exception e)
+		{
+			throw e;
+		}
+	}
+	
+}