Package plugin

Class Descriptor_based_registration

java.lang.Object
plugin.Descriptor_based_registration
All Implemented Interfaces:
ij.plugin.PlugIn
public class Descriptor_based_registration extends Object implements ij.plugin.PlugIn

  • Field Details

    • defaultImg1

      public static int defaultImg1

    • defaultImg2

      public static int defaultImg2

    • defaultReApply

      public static boolean defaultReApply

    • lastModel1

      public static mpicbg.models.InvertibleBoundable lastModel1

    • lastModel2

      public static mpicbg.models.InvertibleBoundable lastModel2

    • lastDimensionality

      public static int lastDimensionality

    • transformationModels2d

      public String[] transformationModels2d

    • transformationModels3d

      public String[] transformationModels3d

    • defaultTransformationModel

      public static int defaultTransformationModel

    • defaultRegularizationTransformationModel

      public static int defaultRegularizationTransformationModel

    • defaultLambda

      public static double defaultLambda

    • defaultFixFirstTile

      public static boolean defaultFixFirstTile

    • defaultRegularize

      public static boolean defaultRegularize

    • detectionBrightness

      public static String[] detectionBrightness

    • defaultDetectionBrightness

      public static int defaultDetectionBrightness

    • defaultSigma

      public static double defaultSigma

    • defaultThreshold

      public static double defaultThreshold

    • detectionSize

      public static String[] detectionSize

    • defaultDetectionSize

      public static int defaultDetectionSize

    • detectionTypes

      public static String[] detectionTypes

    • defaultDetectionType

      public static int defaultDetectionType

    • defaultInteractiveMaxima

      public static boolean defaultInteractiveMaxima

    • defaultInteractiveMinima

      public static boolean defaultInteractiveMinima

    • defaultSensitivity

      public static final int defaultSensitivity
      See Also:

    • orientation

      public static String[] orientation

    • defaultSimilarOrientation

      public static int defaultSimilarOrientation

    • defaultNumNeighbors

      public static int defaultNumNeighbors

    • defaultRedundancy

      public static int defaultRedundancy

    • defaultSignificance

      public static double defaultSignificance

    • defaultRansacThreshold

      public static double defaultRansacThreshold

    • defaultChannel1

      public static int defaultChannel1

    • defaultChannel2

      public static int defaultChannel2

    • defaultCreateOverlay

      public static boolean defaultCreateOverlay

    • defaultAddPointRoi

      public static boolean defaultAddPointRoi

    • axes

      public String[] axes

    • defaultAxis1

      public static int defaultAxis1

    • defaultAxis2

      public static int defaultAxis2

    • defaultAxis3

      public static int defaultAxis3

    • defaultDegrees1

      public static double defaultDegrees1

    • defaultDegrees2

      public static double defaultDegrees2

    • defaultDegrees3

      public static double defaultDegrees3

    • defaultScale

      public static double defaultScale

    • m00

      public static double m00

    • m01

      public static double m01

    • m02

      public static double m02

    • m03

      public static double m03

    • m10

      public static double m10

    • m11

      public static double m11

    • m12

      public static double m12

    • m13

      public static double m13

    • m20

      public static double m20

    • m21

      public static double m21

    • m22

      public static double m22

    • m23

      public static double m23

  • Constructor Details

    • Descriptor_based_registration

      public Descriptor_based_registration()

  • Method Details

    • run

      public void run(String arg0)
      Specified by:
      run in interface ij.plugin.PlugIn

    • getParameters

      protected DescriptorParameters getParameters(ij.ImagePlus imp1, ij.ImagePlus imp2, int dimensionality)
      Ask for all other required parameters ..
      Parameters:
      dimensionality -

    • getAdvancedDoGParameters

      protected static double[] getAdvancedDoGParameters(double defaultSigma, double defaultThreshold)

    • getInteractiveDoGParameters

      public static net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoGParams getInteractiveDoGParameters(ij.ImagePlus imp, int channel, double[] values, float sigmaMax)
      Can be called with values[ 3 ], i.e. [initialsigma, sigma2, threshold] or values[ 2 ], i.e. [initialsigma, threshold]. The results are stored in the same array. Adapted to the rewritten interactive DoG of multiview-reconstruction 9.x (InteractiveDoG + InteractiveDoGParams): the GUI exposes only sigma, threshold and look-for-maxima/minima, and reports the result back through the params object. NB: the new GUI uses a fixed sigma slider range (see InteractiveDoG.sigmaMax); the sigmaMax argument is no longer honored. sigma2 is always derived from sigma1.
      Parameters:
      imp - - the image to detect on (must be displayed; its window provides the preview canvas)
      channel - - the channel (0-based) to run the interactive detection on
      values - - the initial values; on success it also receives the result
      sigmaMax - - kept for source compatibility; no longer honored by the new GUI
      Returns:
      the InteractiveDoGParams with the chosen parameters, or null if canceled

    • getInteractiveDoGParameters

      public static net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoGParams getInteractiveDoGParameters(ij.ImagePlus imp, int channel, double[] values, float sigmaMax, float[] minmaxOverride)
      Parameters:
      minmaxOverride - - if non-null, the intensity range [ min, max ] used to normalize the preview, so the interactively tuned threshold matches the actual detection (global/user-defined modes); if null, the auto display range of the preview is used (local mode).

    • testRegistrationCompatibility

      public static String testRegistrationCompatibility(ij.ImagePlus imp1, ij.ImagePlus imp2)