Examples with Workspaces io.github.mianalysis.mia.object.Workspaces used on opensource projects

Example 1 with Workspaces

use of io.github.mianalysis.mia.object.Workspaces in project mia by mianalysis.

the class Exporter method exportResults.

public void exportResults(Workspace workspace, Analysis analysis, String name) throws IOException {
    Workspaces currentWorkspaces = new Workspaces();
    currentWorkspaces.add(workspace);
    export(currentWorkspaces, analysis, name);
}

Example 2 with Workspaces

use of io.github.mianalysis.mia.object.Workspaces in project mia by mianalysis.

the class GUI method updateProgressBar.

public static synchronized void updateProgressBar() {
    Workspaces workspaces = analysisRunner.getWorkspaces();
    updateProgressBar((int) Math.round(workspaces.getOverallProgress() * 100));
}

Example 3 with Workspaces

use of io.github.mianalysis.mia.object.Workspaces in project mia by mianalysis.

the class NormaliseIntensityTest method testNormaliseIntensity8bit2D.

@Test
public void testNormaliseIntensity8bit2D() throws Exception {
    // Creating a new workspace
    Workspaces workspaces = new Workspaces();
    Workspace workspace = workspaces.getNewWorkspace(null, 1);
    // Loading the test image and adding to workspace
    String pathToImage = URLDecoder.decode(this.getClass().getResource("/images/normaliseintensity/DarkNoisyGradient2D_8bit.zip").getPath(), "UTF-8");
    ImagePlus ipl = IJ.openImage(pathToImage);
    Image image = new Image("Test_image", ipl);
    workspace.addImage(image);
    pathToImage = URLDecoder.decode(this.getClass().getResource("/images/normaliseintensity/DarkNoisyGradientNormalised2D_8bit.zip").getPath(), "UTF-8");
    Image expectedImage = new Image("Expected", IJ.openImage(pathToImage));
    // Initialising BinaryOperations
    NormaliseIntensity normaliseIntensity = new NormaliseIntensity(new Modules());
    normaliseIntensity.updateParameterValue(NormaliseIntensity.INPUT_IMAGE, "Test_image");
    normaliseIntensity.updateParameterValue(NormaliseIntensity.APPLY_TO_INPUT, false);
    normaliseIntensity.updateParameterValue(NormaliseIntensity.OUTPUT_IMAGE, "Test_output");
    // Running NormaliseIntensity
    normaliseIntensity.execute(workspace);
    // Checking the images in the workspace
    assertEquals(2, workspace.getImages().size());
    assertNotNull(workspace.getImage("Test_image"));
    assertNotNull(workspace.getImage("Test_output"));
    // Checking the output image has the expected calibration
    Image outputImage = workspace.getImage("Test_output");
    assertEquals(expectedImage, outputImage);
}

Example 4 with Workspaces

use of io.github.mianalysis.mia.object.Workspaces in project mia by mianalysis.

the class NormaliseIntensityTest method testNormaliseIntensity16bit3D.

@Test
public void testNormaliseIntensity16bit3D() throws Exception {
    // Creating a new workspace
    Workspaces workspaces = new Workspaces();
    Workspace workspace = workspaces.getNewWorkspace(null, 1);
    // Loading the test image and adding to workspace
    String pathToImage = URLDecoder.decode(this.getClass().getResource("/images/normaliseintensity/DarkNoisyGradient3D_16bit.zip").getPath(), "UTF-8");
    ImagePlus ipl = IJ.openImage(pathToImage);
    Image image = new Image("Test_image", ipl);
    workspace.addImage(image);
    pathToImage = URLDecoder.decode(this.getClass().getResource("/images/normaliseintensity/DarkNoisyGradientNormalised3D_16bit.zip").getPath(), "UTF-8");
    Image expectedImage = new Image("Expected", IJ.openImage(pathToImage));
    // Initialising BinaryOperations
    NormaliseIntensity normaliseIntensity = new NormaliseIntensity(new Modules());
    normaliseIntensity.updateParameterValue(NormaliseIntensity.INPUT_IMAGE, "Test_image");
    normaliseIntensity.updateParameterValue(NormaliseIntensity.APPLY_TO_INPUT, false);
    normaliseIntensity.updateParameterValue(NormaliseIntensity.OUTPUT_IMAGE, "Test_output");
    // Running NormaliseIntensity
    normaliseIntensity.execute(workspace);
    // Checking the images in the workspace
    assertEquals(2, workspace.getImages().size());
    assertNotNull(workspace.getImage("Test_image"));
    assertNotNull(workspace.getImage("Test_output"));
    // Checking the output image has the expected calibration
    Image outputImage = workspace.getImage("Test_output");
    assertEquals(expectedImage, outputImage);
}

Example 5 with Workspaces

use of io.github.mianalysis.mia.object.Workspaces in project mia by mianalysis.

the class NormaliseIntensityTest method testNormaliseIntensity32bitUnderOne3D.

@Test
public void testNormaliseIntensity32bitUnderOne3D() throws Exception {
    // Creating a new workspace
    Workspaces workspaces = new Workspaces();
    Workspace workspace = workspaces.getNewWorkspace(null, 1);
    // Loading the test image and adding to workspace
    String pathToImage = URLDecoder.decode(this.getClass().getResource("/images/normaliseintensity/DarkNoisyGradient3D_32bit.zip").getPath(), "UTF-8");
    ImagePlus ipl = IJ.openImage(pathToImage);
    Image image = new Image("Test_image", ipl);
    workspace.addImage(image);
    pathToImage = URLDecoder.decode(this.getClass().getResource("/images/normaliseintensity/DarkNoisyGradientNormalised3D_32bit.zip").getPath(), "UTF-8");
    Image expectedImage = new Image("Expected", IJ.openImage(pathToImage));
    // Initialising BinaryOperations
    NormaliseIntensity normaliseIntensity = new NormaliseIntensity(new Modules());
    normaliseIntensity.updateParameterValue(NormaliseIntensity.INPUT_IMAGE, "Test_image");
    normaliseIntensity.updateParameterValue(NormaliseIntensity.APPLY_TO_INPUT, false);
    normaliseIntensity.updateParameterValue(NormaliseIntensity.OUTPUT_IMAGE, "Test_output");
    // Running NormaliseIntensity
    normaliseIntensity.execute(workspace);
    // Checking the images in the workspace
    assertEquals(2, workspace.getImages().size());
    assertNotNull(workspace.getImage("Test_image"));
    assertNotNull(workspace.getImage("Test_output"));
    // Checking the output image has the expected calibration
    Image outputImage = workspace.getImage("Test_output");
    assertEquals(expectedImage, outputImage);
}