Descriptor_based_registration (Fiji Javadocs 0-SNAPSHOT API)

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 Summary

Fields
Modifier and Type	Field and Description
`String[]`	`axes`
`static boolean`	`defaultAddPointRoi`
`static int`	`defaultAxis1`
`static int`	`defaultAxis2`
`static int`	`defaultAxis3`
`static int`	`defaultChannel1`
`static int`	`defaultChannel2`
`static boolean`	`defaultCreateOverlay`
`static double`	`defaultDegrees1`
`static double`	`defaultDegrees2`
`static double`	`defaultDegrees3`
`static int`	`defaultDetectionBrightness`
`static int`	`defaultDetectionSize`
`static int`	`defaultDetectionType`
`static boolean`	`defaultFixFirstTile`
`static int`	`defaultImg1`
`static int`	`defaultImg2`
`static boolean`	`defaultInteractiveMaxima`
`static boolean`	`defaultInteractiveMinima`
`static double`	`defaultLambda`
`static int`	`defaultNumNeighbors`
`static double`	`defaultRansacThreshold`
`static boolean`	`defaultReApply`
`static int`	`defaultRedundancy`
`static int`	`defaultRegularizationTransformationModel`
`static boolean`	`defaultRegularize`
`static double`	`defaultScale`
`static double`	`defaultSigma`
`static double`	`defaultSignificance`
`static int`	`defaultSimilarOrientation`
`static double`	`defaultThreshold`
`static int`	`defaultTransformationModel`
`static String[]`	`detectionBrightness`
`static String[]`	`detectionSize`
`static String[]`	`detectionTypes`
`static int`	`lastDimensionality`
`static InvertibleBoundable`	`lastModel1`
`static InvertibleBoundable`	`lastModel2`
`static double`	`m00`
`static double`	`m01`
`static double`	`m02`
`static double`	`m03`
`static double`	`m10`
`static double`	`m11`
`static double`	`m12`
`static double`	`m13`
`static double`	`m20`
`static double`	`m21`
`static double`	`m22`
`static double`	`m23`
`static String[]`	`orientation`
`String[]`	`transformationModels2d`
`String[]`	`transformationModels3d`

Constructor Summary

Constructors
Constructor and Description

Descriptor_based_registration()

Constructors
Constructor and Description
`Descriptor_based_registration()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected static double[]`	`getAdvancedDoGParameters(double defaultSigma, double defaultThreshold)`
`static InteractiveDoG`	`getInteractiveDoGParameters(ij.ImagePlus imp, int channel, double[] values, float sigmaMax)` Can be called with values[ 3 ], i.e.
`protected DescriptorParameters`	`getParameters(ij.ImagePlus imp1, ij.ImagePlus imp2, int dimensionality)` Ask for all other required parameters ..
`void`	`run(String arg0)`
`static String`	`testRegistrationCompatibility(ij.ImagePlus imp1, ij.ImagePlus imp2)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

defaultImg1
```
public static int defaultImg1
```

defaultImg2
```
public static int defaultImg2
```

defaultReApply
```
public static boolean defaultReApply
```

lastModel1

public static InvertibleBoundable lastModel1

lastModel2

public static 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

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 Detail
- Descriptor_based_registration
```
public Descriptor_based_registration()
```

Method Detail

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 InteractiveDoG 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. If called with values[ 2 ], sigma2 changing will be disabled

Parameters:

values - - the initial values and also contains the result

sigmaMax - - the maximal sigma allowed by the interactive app

Returns:

InteractiveDoG - the instance for querying additional parameters

testRegistrationCompatibility

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

Class Descriptor_based_registration

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

defaultImg1

defaultImg2

defaultReApply

lastModel1

lastModel2

lastDimensionality

transformationModels2d

transformationModels3d

defaultTransformationModel

defaultRegularizationTransformationModel

defaultLambda

defaultFixFirstTile

defaultRegularize

detectionBrightness

defaultDetectionBrightness

defaultSigma

defaultThreshold

detectionSize

defaultDetectionSize

detectionTypes

defaultDetectionType

defaultInteractiveMaxima

defaultInteractiveMinima

orientation

defaultSimilarOrientation

defaultNumNeighbors

defaultRedundancy

defaultSignificance

defaultRansacThreshold

defaultChannel1

defaultChannel2

defaultCreateOverlay

defaultAddPointRoi

axes

defaultAxis1

defaultAxis2

defaultAxis3

defaultDegrees1

defaultDegrees2

defaultDegrees3

defaultScale

m00

m01

m02

m03

m10

m11

m12

m13

m20

m21

m22

m23

Constructor Detail

Descriptor_based_registration

Method Detail

run

getParameters

getAdvancedDoGParameters

getInteractiveDoGParameters

testRegistrationCompatibility