ExtractPSF (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.spim.postprocessing.deconvolution.ExtractPSF

```
public class ExtractPSF
extends Object
```

Constructor Summary

Constructors
Constructor and Description

ExtractPSF(SPIMConfiguration config)

ExtractPSF(ViewStructure viewStructure)

Constructors
Constructor and Description
`ExtractPSF(SPIMConfiguration config)`
`ExtractPSF(ViewStructure viewStructure)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static <T extends Type<T>> int[]`	`commonSize(List<Image<T>> images)` Returns the bounding box so that all images can fit in there or null if input is null or input.size is 0
`void`	`computeAveragePSF(int[] maxSize)` compute the average psf in original calibration and after applying the transformations
`void`	`extract()`
`void`	`extract(int viewID, int[] maxSize)`
`protected static Image<FloatType>`	`extractPSF(ViewDataBeads view, int[] size)` Extracts the PSF by averaging the local neighborhood RANSAC correspondences
`Image<FloatType>`	`getAverageOriginalPSF()`
`Image<FloatType>`	`getAveragePSF()`
`Image<FloatType>`	`getMaxProjectionAveragePSF()` Get projection along the smallest dimension (which is usually the rotation axis)
`ArrayList<Image<FloatType>>`	`getPSFs()`
`ArrayList<Image<FloatType>>`	`getPSFsInInputCalibration()`
`static ExtractPSF`	`loadAndTransformPSF(ArrayList<String> fileName, boolean transformPSFs, ViewStructure viewStructure)`
`static Image<FloatType>`	`makeSameSize(Image<FloatType> img, int[] sizeIn)` Make image the same size as defined, center it
`void`	`setPSFSize(int size, boolean isotropic, int[] size3d)` Defines the size of the PSF that is extracted
`protected static Image<FloatType>`	`transformPSF(Image<FloatType> psf, AbstractAffineModel3D<?> model)` Transforms the extracted PSF using the affine transformation of the corresponding view

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

- Constructor Detail
  - ExtractPSF
```
public ExtractPSF(SPIMConfiguration config)
```
  - ExtractPSF
```
public ExtractPSF(ViewStructure viewStructure)
```
- Method Detail
  - setPSFSize
```
public void setPSFSize(int size,
                       boolean isotropic,
                       int[] size3d)
```
    Defines the size of the PSF that is extracted
    
    Parameters:
    
    size - - number of pixels in xy
    
    isotropic - - if isotropic, than same size applies to z (in px), otherwise it is divided by half the z-stretching
  - getPSFs
```
public ArrayList<Image<FloatType>> getPSFs()
```
    Returns:
    
    - the extracted PSFs after applying the transformations of each view
  - getPSFsInInputCalibration
```
public ArrayList<Image<FloatType>> getPSFsInInputCalibration()
```
    Returns:
    
    - the extracted PSFs in original calibration for each view
  - getAveragePSF
```
public Image<FloatType> getAveragePSF()
```
    Returns:
    
    - the average extracted PSF after applying the transformations of each view
  - getAverageOriginalPSF
```
public Image<FloatType> getAverageOriginalPSF()
```
    Returns:
    
    - the average extracted PSF in the same calibration as the input data
  - getMaxProjectionAveragePSF
```
public Image<FloatType> getMaxProjectionAveragePSF()
```
    Get projection along the smallest dimension (which is usually the rotation axis)
    
    Returns:
    
    - the averaged, projected PSF
  - computeAveragePSF
```
public void computeAveragePSF(int[] maxSize)
```
    compute the average psf in original calibration and after applying the transformations
    
    Parameters:
    
    maxSize -
  - extract
```
public void extract(int viewID,
                    int[] maxSize)
```
  - extract
```
public void extract()
```
  - transformPSF
```
protected static Image<FloatType> transformPSF(Image<FloatType> psf,
                                               AbstractAffineModel3D<?> model)
```
    Transforms the extracted PSF using the affine transformation of the corresponding view
    
    Parameters:
    
    psf - - the extracted psf (NOT z-scaling corrected)
    
    model - - the transformation model
    
    Returns:
    
    the transformed psf which has odd sizes and where the center of the psf is also the center of the transformed psf
  - extractPSF
```
protected static Image<FloatType> extractPSF(ViewDataBeads view,
                                             int[] size)
```
    Extracts the PSF by averaging the local neighborhood RANSAC correspondences
    
    Parameters:
    
    view - - the SPIM view
    
    size - - the size in which the psf is extracted (in pixel units, z-scaling is ignored)
    
    Returns:
    
    - the psf, NOT z-scaling corrected
  - makeSameSize
```
public static Image<FloatType> makeSameSize(Image<FloatType> img,
                                            int[] sizeIn)
```
    Make image the same size as defined, center it
    
    Parameters:
    
    img -
    
    Returns:
  - commonSize
```
public static <T extends Type<T>> int[] commonSize(List<Image<T>> images)
```
    Returns the bounding box so that all images can fit in there or null if input is null or input.size is 0
    
    Parameters:
    
    images -
    
    Returns:
  - loadAndTransformPSF
```
public static ExtractPSF loadAndTransformPSF(ArrayList<String> fileName,
                                             boolean transformPSFs,
                                             ViewStructure viewStructure)
```

Class ExtractPSF

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ExtractPSF

ExtractPSF

Method Detail

setPSFSize

getPSFs

getPSFsInInputCalibration

getAveragePSF

getAverageOriginalPSF

getMaxProjectionAveragePSF

computeAveragePSF

extract

extract

transformPSF

extractPSF

makeSameSize

commonSize

loadAndTransformPSF