| Package | Description |
|---|---|
| mpicbg.imglib.image.display.imagej | |
| mpicbg.models | |
| mpicbg.stitching.fusion | |
| plugin | |
| process |
| Modifier and Type | Method and Description |
|---|---|
InvertibleBoundable |
InverseTransformDescription.getTransform() |
| Constructor and Description |
|---|
InverseTransformDescription(InvertibleBoundable transform,
InterpolatorFactory<T> factory,
Image<T> image) |
| Modifier and Type | Class and Description |
|---|---|
class |
ConstantAffineModel1D<A extends Model<A> & Affine1D<A> & InvertibleBoundable>
1D affine specialization of
ConstantModel. |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractAffineModel1D<M extends AbstractAffineModel1D<M>> |
class |
AbstractAffineModel2D<M extends AbstractAffineModel2D<M>> |
class |
AbstractAffineModel3D<M extends AbstractAffineModel3D<M>> |
class |
AffineModel1D |
class |
AffineModel2D
2d-affine transformation models to be applied to points in 2d-space.
|
class |
AffineModel3D
3d-affine transformation models to be applied to points in 3d-space.
|
class |
ConstantAffineModel1D<A extends Model<A> & Affine1D<A> & InvertibleBoundable>
1D affine specialization of
ConstantModel. |
class |
HomographyModel2D
2d-homography
AbstractModel to be applied to points in 2d-space. |
class |
IdentityModel
nd-identity
AbstractModel. |
class |
InterpolatedAffineModel1D<A extends Model<A> & Affine1D<A>,B extends Model<B> & Affine1D<B>>
1D affine specialization of
InterpolatedModel. |
class |
InterpolatedAffineModel2D<A extends Model<A> & Affine2D<A>,B extends Model<B> & Affine2D<B>>
2D affine specialization of
InterpolatedModel. |
class |
InterpolatedAffineModel3D<A extends Model<A> & Affine3D<A>,B extends Model<B> & Affine3D<B>>
3D affine specialization of
InterpolatedModel. |
class |
InvertibleCoordinateTransformList<E extends InvertibleCoordinateTransform> |
class |
RigidModel2D
2d-rigid transformation models to be applied to points in 2d-space.
|
class |
RigidModel3D |
class |
SimilarityModel2D
2d-similarity transformation models to be applied to points in 2d-space.
|
class |
SimilarityModel3D
3d-rigid transformation models to be applied to points in 3d-space.
|
class |
TranslationModel1D
1d-translation
AbstractModel to be applied to points in 1d-space. |
class |
TranslationModel2D
2d-translation
AbstractModel to be applied to points in 2d-space. |
class |
TranslationModel3D |
| Modifier and Type | Method and Description |
|---|---|
protected static <T extends RealType<T> & NativeType<T>> |
OverlayFusion.createOverlay(T targetType,
ij.ImagePlus imp1,
ij.ImagePlus imp2,
InvertibleBoundable finalModel1,
InvertibleBoundable finalModel2,
int dimensionality) |
| Modifier and Type | Method and Description |
|---|---|
static <T extends RealType<T> & NativeType<T>> |
OverlayFusion.createOverlay(T targetType,
ArrayList<ij.ImagePlus> images,
ArrayList<InvertibleBoundable> models,
int dimensionality,
int timepoint,
InterpolatorFactory<FloatType,RandomAccessible<FloatType>> factory) |
static <T extends RealType<T> & NativeType<T>> |
OverlayFusion.createReRegisteredSeries(T targetType,
ij.ImagePlus imp,
ArrayList<InvertibleBoundable> models,
int dimensionality) |
static void |
Fusion.estimateBounds(double[] offset,
int[] size,
int[][] imgSizes,
ArrayList<InvertibleBoundable> models,
int dimensionality)
Estimate the bounds of the output image.
|
static void |
Fusion.estimateBounds(double[] offset,
int[] size,
List<ij.ImagePlus> images,
ArrayList<InvertibleBoundable> models,
int dimensionality)
Estimate the bounds of the output image.
|
static <T extends RealType<T> & NativeType<T>> |
Fusion.fuse(T targetType,
ArrayList<ij.ImagePlus> images,
ArrayList<InvertibleBoundable> models,
int dimensionality,
boolean subpixelResolution,
int fusionType,
String outputDirectory,
boolean noOverlap,
boolean ignoreZeroValues,
boolean displayImages) |
protected static <T extends RealType<T>> |
Fusion.fuseBlock(Img<T> output,
ArrayList<? extends ImageInterpolation<? extends RealType<?>>> input,
double[] offset,
ArrayList<InvertibleBoundable> transform,
PixelFusion fusion,
boolean displayFusion)
Fuse one slice/volume (one channel)
|
protected static <T extends RealType<T>> |
Fusion.fuseBlockNoOverlap(Img<T> output,
ArrayList<? extends ImageInterpolation<? extends RealType<?>>> input,
double[] offset,
ArrayList<InvertibleBoundable> transform,
boolean displayFusion)
Fuse one slice/volume (one channel)
|
protected static <T extends RealType<T>> |
Fusion.writeBlock(Img<T> outputSlice,
int numSlices,
int t,
int numTimePoints,
int c,
int numChannels,
ArrayList<? extends ImageInterpolation<? extends RealType<?>>> input,
double[] offset,
ArrayList<InvertibleBoundable> transform,
PixelFusion fusion,
String outputDirectory)
Fuse one slice/volume (one channel)
|
| Modifier and Type | Field and Description |
|---|---|
static InvertibleBoundable |
Descriptor_based_registration.lastModel1 |
static InvertibleBoundable |
Descriptor_based_registration.lastModel2 |
InvertibleBoundable |
DescriptorParameters.model1 |
InvertibleBoundable |
DescriptorParameters.model2 |
| Modifier and Type | Field and Description |
|---|---|
static ArrayList<InvertibleBoundable> |
Descriptor_based_series_registration.lastModels |
| Modifier and Type | Method and Description |
|---|---|
protected static <T extends RealType<T> & NativeType<T>> |
Stitching_Pairwise.fuse(T targetType,
ij.ImagePlus imp1,
ij.ImagePlus imp2,
ArrayList<InvertibleBoundable> models,
StitchingParameters params) |
| Modifier and Type | Method and Description |
|---|---|
static ArrayList<InvertibleBoundable> |
Matching.descriptorBasedStackRegistration(ij.ImagePlus imp,
DescriptorParameters params) |
static ArrayList<InvertibleBoundable> |
Matching.globalOptimization(Vector<ComparePair> pairs,
int numImages,
DescriptorParameters params) |
| Modifier and Type | Method and Description |
|---|---|
protected static <T extends RealType<T>> |
OverlayFusion.createOverlay(T targetType,
ij.ImagePlus imp1,
ij.ImagePlus imp2,
InvertibleBoundable finalModel1,
InvertibleBoundable finalModel2,
int dimensionality,
int interpolation) |
| Modifier and Type | Method and Description |
|---|---|
static <T extends RealType<T>> |
OverlayFusion.createOverlay(T targetType,
ArrayList<ij.ImagePlus> images,
ArrayList<InvertibleBoundable> models,
int dimensionality,
int timepoint,
InterpolatorFactory<FloatType> factory) |
static <T extends RealType<T>> |
OverlayFusion.createReRegisteredSeries(T targetType,
ij.ImagePlus imp,
ArrayList<InvertibleBoundable> models,
int dimensionality,
String directory,
int interpolation) |
static void |
OverlayFusion.estimateBounds(float[] offset,
int[] size,
int[][] imgSizes,
ArrayList<InvertibleBoundable> models,
int dimensionality)
Estimate the bounds of the output image.
|
static void |
OverlayFusion.estimateBounds(float[] offset,
int[] size,
List<ij.ImagePlus> images,
ArrayList<InvertibleBoundable> models,
int dimensionality)
Estimate the bounds of the output image.
|
protected static int |
Matching.performIteration(ArrayList<InvertibleBoundable> lastModels,
ArrayList<ArrayList<DifferenceOfGaussianPeak<FloatType>>> peaksComplete,
int numImages,
DescriptorParameters params,
float zStretching)
Computes one iteration and updates the lastModels ArrayList with the new models
|
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