SpatialImage (XitoSBML 1.2.0 API)

java.lang.Object
- jp.ac.keio.bio.fun.xitosbml.image.SpatialImage

```
public class SpatialImage
extends Object
```
The class SpatialImage, which is a class for handling spatial image in XitoSBML. Date Created: Feb 21, 2017

Author:

Kaito Ii <ii@fun.bio.keio.ac.jp>, Akira Funahashi <funa@bio.keio.ac.jp>

Field Summary

Fields
Modifier and Type Field and Description

String title
The title of the image.

Fields
Modifier and Type	Field and Description
`String`	`title` The title of the image.

Constructor Summary

Constructors
Constructor and Description
`SpatialImage(HashMap<String,Integer> hashSampledValue, HashMap<String,Integer> hashDomainTypes, ij.ImagePlus img)` Instantiates a new spatial image with given image object.
`SpatialImage(HashMap<String,Integer> hashSampledValue, ij.ImagePlus img)` Instantiates a new spatial image given image object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`createHashDomainTypes()` Creates the hashmap of domain types of spatial image.
`ArrayList<ArrayList<String>>`	`getAdjacentsList()` Gets the list of adjacent of spatial image.
`org.scijava.vecmath.Point3d`	`getDelta()` Gets the delta of spatial image.
`int`	`getDepth()` Gets the depth of spatial image.
`HashMap<String,Integer>`	`getHashDomainNum()` Gets the hashmap of the count number of domains in each domain types.
`HashMap<String,Integer>`	`getHashDomainTypes()` Gets the hashmap of domain types of spatial image.
`HashMap<String,org.scijava.vecmath.Point3d>`	`getHashDomInteriorPt()` Gets the hashmap of domain InteriorPoint of spatial image.
`HashMap<String,Integer>`	`getHashSampledValue()` Gets the hash sampled value of spatial image.
`int`	`getHeight()` Gets the height of spatial image.
`ij.ImagePlus`	`getImage()` Gets the ImageJ image object.
`byte[]`	`getRaw()` Gets the raw data of spatial image in 1D array.
`String`	`getUnit()` Gets the unit of a CoordinateComponent.
`int`	`getWidth()` Gets the width of spatial image.
`void`	`saveAsImage(String path, String name)` Save image as TIFF file.
`void`	`setAdjacentsList(ArrayList<ArrayList<String>> adjacentsList)` Sets the list of adjacent of spatial image.
`void`	`setDelta(org.scijava.vecmath.Point3d delta)` Sets the delta of spatial image.
`void`	`setDepth(int depth)` Sets the depth of spatial image with given depth value.
`void`	`setHashDomainNum(HashMap<String,Integer> hashDomainNum)` Sets the hashmap of the count number of domains in each domain types with given HashMap<String, Integer>
`void`	`setHashDomainTypes(HashMap<String,Integer> hashDomainTypes)` Sets the hashmap of domain types.
`void`	`setHashDomInteriorpt(HashMap<String,org.scijava.vecmath.Point3d> hashDomInteriorPt)` Sets the hashmap of domain InteriorPoint of spatial image.
`void`	`setHashSampledValue(HashMap<String,Integer> hashSampledValue)` Sets the hashmap of sampled value of spatial image.
`void`	`setHeight(int height)` Sets the height of spatial image with given height value.
`void`	`setImage(ij.ImagePlus image)` Sets the image object and create 1D array of the image and sets to raw object.
`void`	`setRaw(byte[] raw)` Sets the raw data of spatial image in 1D array.
`void`	`setUnit()` Sets the unit of a CoordinateComponent.
`void`	`setWidth(int width)` Sets the width of spatial image with given width value.
`void`	`updateImage(ij.ImageStack imStack)` Update image with given stack of images.

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

- Field Detail
  - title
```
public String title
```
    The title of the image.
- Constructor Detail
  - SpatialImage
```
public SpatialImage(HashMap<String,Integer> hashSampledValue,
                    HashMap<String,Integer> hashDomainTypes,
                    ij.ImagePlus img)
```
    Instantiates a new spatial image with given image object. SpatialImage object is generated with given image, sampled value (pixel value of a SampledVolume) and domain types. Unit of spatial image will be adjusted by reading file information from given image.
    
    Parameters:
    
    hashSampledValue - the hashmap of sampled value, that is a pixel value of a SampledVolume
    
    hashDomainTypes - the hashmap of domain types
    
    img - the image as an ImageJ object
  - SpatialImage
```
public SpatialImage(HashMap<String,Integer> hashSampledValue,
                    ij.ImagePlus img)
```
    Instantiates a new spatial image given image object. SpatialImage object is generated with given image and sampled value (pixel value of a SampledVolume). Unit of spatial image will be adjusted by reading file information from given image.
    
    Parameters:
    
    hashSampledValue - the hashmap of sampled value, that is a pixel value of a SampledVolume
    
    img - the image as an ImageJ object
- Method Detail
  - setImage
```
public void setImage(ij.ImagePlus image)
```
    Sets the image object and create 1D array of the image and sets to raw object.
    
    Parameters:
    
    image - the new image as an ImageJ object
  - getImage
```
public ij.ImagePlus getImage()
```
    Gets the ImageJ image object.
    
    Returns:
    
    the image as an ImageJ object
  - updateImage
```
public void updateImage(ij.ImageStack imStack)
```
    Update image with given stack of images. The raw data (1D array) will be also updated.
    
    Parameters:
    
    imStack - the stack of images (ImageStack) object
  - getWidth
```
public int getWidth()
```
    Gets the width of spatial image.
    
    Returns:
    
    the width of spatial image
  - setWidth
```
public void setWidth(int width)
```
    Sets the width of spatial image with given width value.
    
    Parameters:
    
    width - the new width of spatial image
  - getHeight
```
public int getHeight()
```
    Gets the height of spatial image.
    
    Returns:
    
    the height of spatial image
  - setHeight
```
public void setHeight(int height)
```
    Sets the height of spatial image with given height value.
    
    Parameters:
    
    height - the new height of spatial image
  - getDepth
```
public int getDepth()
```
    Gets the depth of spatial image.
    
    Returns:
    
    the depth of spatial image
  - setDepth
```
public void setDepth(int depth)
```
    Sets the depth of spatial image with given depth value.
    
    Parameters:
    
    depth - the new depth of spatial image
  - getHashSampledValue
```
public HashMap<String,Integer> getHashSampledValue()
```
    Gets the hash sampled value of spatial image.
    
    Returns:
    
    the hash sampled value of spatial image
  - setHashSampledValue
```
public void setHashSampledValue(HashMap<String,Integer> hashSampledValue)
```
    Sets the hashmap of sampled value of spatial image. HashMap<String, Integer>
    
    Parameters:
    
    hashSampledValue - the hash sampled value of spatial image
  - getRaw
```
public byte[] getRaw()
```
    Gets the raw data of spatial image in 1D array.
    
    Returns:
    
    the raw data (1D array) of spatial image
  - setRaw
```
public void setRaw(byte[] raw)
```
    Sets the raw data of spatial image in 1D array.
    
    Parameters:
    
    raw - the new raw data of spatial image in 1D array
  - getHashDomainTypes
```
public HashMap<String,Integer> getHashDomainTypes()
```
    Gets the hashmap of domain types of spatial image.
    
    Returns:
    
    the hashmap of domain types of spatial image
  - setHashDomainTypes
```
public void setHashDomainTypes(HashMap<String,Integer> hashDomainTypes)
```
    Sets the hashmap of domain types. HashMap<String, Integer>
    
    Parameters:
    
    hashDomainTypes - the hashmap of domain types of spatial image
  - createHashDomainTypes
```
public void createHashDomainTypes()
```
    Creates the hashmap of domain types of spatial image. The value of domain type (spatialDimensions) will be set depending on the value of spatial ID reference (SpIdRef).
  - getHashDomainNum
```
public HashMap<String,Integer> getHashDomainNum()
```
    Gets the hashmap of the count number of domains in each domain types. HashMap<String, Integer>
    
    Returns:
    
    hashDomainNum the hashmap of the count number of domains in each domain types
  - setHashDomainNum
```
public void setHashDomainNum(HashMap<String,Integer> hashDomainNum)
```
    Sets the hashmap of the count number of domains in each domain types with given HashMap<String, Integer>
    
    Parameters:
    
    hashDomainNum - the hashmap of the count number of domains in each domain types
  - getAdjacentsList
```
public ArrayList<ArrayList<String>> getAdjacentsList()
```
    Gets the list of adjacent of spatial image.
    
    Returns:
    
    the list of adjacent of spatial image
  - setAdjacentsList
```
public void setAdjacentsList(ArrayList<ArrayList<String>> adjacentsList)
```
    Sets the list of adjacent of spatial image.
    
    Parameters:
    
    adjacentsList - the new list of adjacent of spatial image
  - saveAsImage
```
public void saveAsImage(String path,
                        String name)
```
    Save image as TIFF file. Both 2D and 3D TIFF images are supported.
    
    Parameters:
    
    path - the path to the directory
    
    name - the name of TIFF file
  - getUnit
```
public String getUnit()
```
    Gets the unit of a CoordinateComponent.
    
    Returns:
    
    the unit of a CoordinateComponent
  - setUnit
```
public void setUnit()
```
    Sets the unit of a CoordinateComponent.
  - getDelta
```
public org.scijava.vecmath.Point3d getDelta()
```
    Gets the delta of spatial image.
    
    Returns:
    
    the delta of spatial image
  - setDelta
```
public void setDelta(org.scijava.vecmath.Point3d delta)
```
    Sets the delta of spatial image.
    
    Parameters:
    
    delta - the new delta of spatial image
  - getHashDomInteriorPt
```
public HashMap<String,org.scijava.vecmath.Point3d> getHashDomInteriorPt()
```
    Gets the hashmap of domain InteriorPoint of spatial image.
    
    Returns:
    
    the hashmap of domain InteriorPoint of spatial image
  - setHashDomInteriorpt
```
public void setHashDomInteriorpt(HashMap<String,org.scijava.vecmath.Point3d> hashDomInteriorPt)
```
    Sets the hashmap of domain InteriorPoint of spatial image.
    
    Parameters:
    
    hashDomInteriorPt - the hashmap of domain InteriroPoint of spatial image

Class SpatialImage

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

title

Constructor Detail

SpatialImage

SpatialImage

Method Detail

setImage

getImage

updateImage

getWidth

setWidth

getHeight

setHeight

getDepth

setDepth

getHashSampledValue

setHashSampledValue

getRaw

setRaw

getHashDomainTypes

setHashDomainTypes

createHashDomainTypes

getHashDomainNum

setHashDomainNum

getAdjacentsList

setAdjacentsList

saveAsImage

getUnit

setUnit

getDelta

setDelta

getHashDomInteriorPt

setHashDomInteriorpt