| Package | Description |
|---|---|
| ini.trakem2.display | |
| ini.trakem2.io | |
| lenscorrection | |
| mpicbg.trakem2.align | |
| mpicbg.trakem2.transform | |
| register_virtual_stack |
| Modifier and Type | Field and Description |
|---|---|
CoordinateTransform |
Patch.TransformProperties.ct |
| Modifier and Type | Method and Description |
|---|---|
CoordinateTransform |
Patch.fetchCoordinateTransform()
Read in the
CoordinateTransform from a file whose name is crafted
from the Patch.ct_id and this Patch's DBObject.id. |
CoordinateTransform |
Patch.getCoordinateTransform()
Obtain a copy of the
CoordinateTransform that transfers image data to mipmap image data. |
CoordinateTransform |
Patch.getFullCoordinateTransform()
Create a
CoordinateTransform that incorporates both the
CoordinateTransform of this Patch (if present) and its
AffineTransform. |
| Modifier and Type | Method and Description |
|---|---|
void |
Patch.appendCoordinateTransform(CoordinateTransform ct)
Append a
CoordinateTransform to the current
CoordinateTransformList. |
protected static Rectangle |
Patch.getCoordinateTransformBoundingBox(Patch p,
CoordinateTransform ct)
Allow reusing a
CoordinateTransform that was already loaded from a file. |
void |
Patch.preAppendCoordinateTransform(CoordinateTransform ct)
Pre-append a
CoordinateTransform to the current
CoordinateTransformList. |
void |
Patch.setCoordinateTransform(CoordinateTransform ct)
Set a CoordinateTransform to this Patch.
|
Bureaucrat |
Display.setCoordinateTransform(List<Patch> patches,
CoordinateTransform ct,
boolean append)
Deprecated.
Use
Display.setCoordinateTransform(List, CoordinateTransform, int) instead which implements pre-appending as a third mode. |
Bureaucrat |
Display.setCoordinateTransform(List<Patch> patches,
CoordinateTransform ct,
int existingTransform) |
void |
Patch.setCoordinateTransformSilently(CoordinateTransform ct)
For reconstruction purposes, overwrites the present
CoordinateTransform, if any, with the given one. |
protected boolean |
Patch.setNewCoordinateTransform(CoordinateTransform ct)
Writes the
CoordinateTransform t to the trakem2.transforms/ directory, using the unique Patch.ct_id
and this Patch's DBObject.id to generate a file path for it. |
static double[] |
Patch.toPixelCoordinate(double world_x,
double world_y,
AffineTransform aff,
CoordinateTransform ct,
int meshResolution,
int o_width,
int o_height) |
| Modifier and Type | Method and Description |
|---|---|
static CoordinateTransform |
CoordinateTransformXML.parse(String xmlPath) |
| Modifier and Type | Field and Description |
|---|---|
protected CoordinateTransform |
DistortionCorrectionTask.SetCoordinateTransformThread.transform |
protected CoordinateTransform |
DistortionCorrectionTask.AppendCoordinateTransformThread.transform |
| Modifier and Type | Method and Description |
|---|---|
protected static void |
DistortionCorrectionTask.appendCoordinateTransform(List<Patch> patches,
CoordinateTransform transform,
int numThreads) |
protected static void |
DistortionCorrectionTask.setCoordinateTransform(List<Patch> patches,
CoordinateTransform transform,
int numThreads) |
| Constructor and Description |
|---|
AppendCoordinateTransformThread(List<Patch> patches,
CoordinateTransform transform,
AtomicInteger ai) |
SetCoordinateTransformThread(List<Patch> patches,
CoordinateTransform transform,
AtomicInteger ai) |
| Modifier and Type | Method and Description |
|---|---|
static void |
Util.applyLayerTransformToPatch(Patch patch,
CoordinateTransform ct) |
protected static void |
ElasticLayerAlignment.applyTransformToLayer(Layer layer,
CoordinateTransform mlt,
Filter<Patch> filter) |
| Modifier and Type | Class and Description |
|---|---|
class |
CoordinateTransformList<E extends CoordinateTransform> |
| Modifier and Type | Interface and Description |
|---|---|
interface |
InvertibleCoordinateTransform
|
| Modifier and Type | Method and Description |
|---|---|
CoordinateTransform |
ThinPlateSplineTransform.copy() |
CoordinateTransform |
CoordinateTransform.copy() |
| Modifier and Type | Method and Description |
|---|---|
static CoordinateTransform |
Register_Virtual_Stack_MT.getCoordinateTransform(Register_Virtual_Stack_MT.Param p)
Get a new coordinate transform given a registration model
|
static CoordinateTransform |
Transform_Virtual_Stack_MT.readCoordinateTransform(String filename)
Read coordinate transform from file (generated in Register_Virtual_Stack)
|
| Modifier and Type | Method and Description |
|---|---|
static ij.ImagePlus |
Transform_Virtual_Stack_MT.applyCoordinateTransform(ij.ImagePlus imp,
CoordinateTransform transform,
int meshResolution,
boolean interpolate,
int[] worldOrigin)
Apply a coordinate transform to a given image
|
static List<PointMatch> |
Register_Virtual_Stack_MT.applyTransformReverse(List<PointMatch> list,
CoordinateTransform t)
Apply a transformation to the second point (P2) of a list of Point matches
|
static boolean |
Register_Virtual_Stack_MT.createResults(String source_dir,
String[] sorted_file_names,
String target_dir,
String save_dir,
CoordinateTransform[] transform,
boolean interpolate)
Create final target images
|
static void |
Register_Virtual_Stack_MT.fitInliers(Register_Virtual_Stack_MT.Param p,
CoordinateTransform t,
List<PointMatch> inliers)
Fit inliers given a registration model
|
static void |
Register_Virtual_Stack_MT.postProcessTransforms(CoordinateTransform[] transform)
Correct transforms from global scaling or rotation
|
static boolean |
Register_Virtual_Stack_MT.register(ij.ImagePlus imp1,
ij.ImagePlus imp2,
ij.ImagePlus imp1mask,
ij.ImagePlus imp2mask,
int i,
String[] sorted_file_names,
String source_dir,
String target_dir,
ExecutorService exe,
Register_Virtual_Stack_MT.Param p,
CoordinateTransform t,
Rectangle commonBounds,
List<Rectangle> bounds,
int referenceIndex)
Register two images with corresponding masks and
following the features and registration models.
|
static void |
Register_Virtual_Stack_MT.regularize(CoordinateTransform t,
int index)
Regularize coordinate transform
|
static boolean |
Register_Virtual_Stack_MT.relax(List<PointMatch>[] inliers,
CoordinateTransform[] transform,
Register_Virtual_Stack_MT.Param p)
Relax inliers
|
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