ReadableHeader (Mango Plugin API)

All Superinterfaces:

MangoPluginType

All Known Subinterfaces:

WritableHeader
```
public interface ReadableHeader
extends MangoPluginType
```
A class that implements ReadableHeader can be registered with Mango to extend the types of image header formats that can be read.

Field Summary

Fields
Modifier and Type Field and Description

static int ORIENTATION_CERTAINTY_HIGH

static int ORIENTATION_CERTAINTY_LOW

static int ORIENTATION_CERTAINTY_MID

Fields
Modifier and Type	Field and Description
`static int`	`ORIENTATION_CERTAINTY_HIGH`
`static int`	`ORIENTATION_CERTAINTY_LOW`
`static int`	`ORIENTATION_CERTAINTY_MID`

Method Summary

Methods
Modifier and Type	Method and Description
`ByteBuffer`	`getImage()` Deprecated.
`ByteBuffer[]`	`getImageBuffers()` Return null to have the application handle reading the image data or return an array of ByteBuffers.
`ImageDescription`	`getImageDescription()` Returns the image description.
`ImageDimensions`	`getImageDimensions()` Returns the image dimensions.
`URI`	`getImageFile()` Returns the image file (could be the same as the header file).
`ImageRange`	`getImageRange()` Returns the image range.
`ImageType`	`getImageType()` Returns the image type.
`String`	`getOrientation()` Returns the orientation (e.g., XYZ+--).
`int`	`getOrientationCertainty()` Returns the orientation certainty (0=Unknown/Default, 1=Incomplete/Suspicious, 2=Complete/Sufficient).
`Coordinate`	`getOrigin()` Returns the origin voxel location relative to the native orientation of the data.
`String`	`getPreferredFileExtension()` Returns the preferred file extension of this format.
`float[]`	`getPreviewImage()` Return null to have the application handle reading the image preview.
`short[]`	`getSliceAnnotation(int slice, int seriesPoint)` Returns a bitmap of annotation data associated with the specified slice.
`String`	`getSliceMetadata(int slice, int seriesPoint)` Returns a formatted text representation of the image header associated with the specified slice.
`ImageTransform[]`	`getTransforms()` Returns an array of any transforms stored in the header.
`VoxelDimensions`	`getVoxelDimensions()` Returns the voxel dimensions.
`boolean`	`isThisFormat(File file)` Used to determine if a file is of this format (e.g., read magic number, check file size, check file extension, etc.).
`void`	`readHeader(File file, File tempDir)` Reads the file.
`void`	`readHeader(URI uri, File tempDir)` Reads the URI.
`String`	`toString()` Returns a formatted text representation of the image header (such as would be displayed in the 'Image Info' window).

Methods inherited from interface edu.uthscsa.ric.mango.MangoPluginType
getMinimumVersionSupported, getPluginName, getPluginURL, getVersion, hasNewerVersion

- Field Detail
  - ORIENTATION_CERTAINTY_HIGH
```
static final int ORIENTATION_CERTAINTY_HIGH
```
    See Also:
    Constant Field Values
  - ORIENTATION_CERTAINTY_LOW
```
static final int ORIENTATION_CERTAINTY_LOW
```
    See Also:
    Constant Field Values
  - ORIENTATION_CERTAINTY_MID
```
static final int ORIENTATION_CERTAINTY_MID
```
    See Also:
    Constant Field Values
- Method Detail
  - getImage
```
@Deprecated
ByteBuffer getImage()
```
    Deprecated.
    
    Return null to have the application handle reading the image data. To handle reading the data yourself (say if the data is not contiguous in the file), return a ByteBuffer which wraps a float array, one float value per voxel
    
    Returns:
    the image buffer or null
  - getImageBuffers
```
ByteBuffer[] getImageBuffers()
```
    Return null to have the application handle reading the image data or return an array of ByteBuffers. Each ByteBuffer must be a FloatBuffer and represent a 3D volume. Multiple buffers represent a series.
    
    Returns:
    the image buffer array or null
  - getImageDescription
```
ImageDescription getImageDescription()
```
    Returns the image description.
    
    Returns:
    the image description
  - getImageDimensions
```
ImageDimensions getImageDimensions()
```
    Returns the image dimensions.
    
    Returns:
    the image dimensions
  - getImageFile
```
URI getImageFile()
```
    Returns the image file (could be the same as the header file).
    
    Returns:
    the image file
  - getImageRange
```
ImageRange getImageRange()
```
    Returns the image range.
    
    Returns:
    the image range
  - getImageType
```
ImageType getImageType()
```
    Returns the image type.
    
    Returns:
    the image type
  - getOrientation
```
String getOrientation()
```
    Returns the orientation (e.g., XYZ+--).
    
    Returns:
    the orientation
  - getOrientationCertainty
```
int getOrientationCertainty()
```
    Returns the orientation certainty (0=Unknown/Default, 1=Incomplete/Suspicious, 2=Complete/Sufficient).
    
    Returns:
    the orientation certainty
  - getOrigin
```
Coordinate getOrigin()
```
    Returns the origin voxel location relative to the native orientation of the data.
    
    Returns:
    the origin
  - getPreferredFileExtension
```
String getPreferredFileExtension()
```
    Returns the preferred file extension of this format.
    
    Returns:
    the preferred file extension
  - getPreviewImage
```
float[] getPreviewImage()
```
    Return null to have the application handle reading the image preview. To create a preview image yourself, return a float array containing one float value per voxel. The float array length should be equal to the number of voxels in a representative slice.
    
    Returns:
    the preview image
  - getTransforms
```
ImageTransform[] getTransforms()
```
    Returns an array of any transforms stored in the header.
    
    Returns:
    an array of any transforms stored in the header (or null if none found)
  - getVoxelDimensions
```
VoxelDimensions getVoxelDimensions()
```
    Returns the voxel dimensions.
    
    Returns:
    the voxel dimensions
  - isThisFormat
```
boolean isThisFormat(File file)
```
    Used to determine if a file is of this format (e.g., read magic number, check file size, check file extension, etc.).
    
    Parameters:
    file - the file to read
    
    Returns:
    returns true if this file can be read by this format, false otherwise
  - readHeader
```
void readHeader(File file,
              File tempDir)
                throws InvalidHeaderException,
                       Exception
```
    Reads the file. The application expects that the image data is contiguous. If it is not, it can be processed into a contiguous file and stored in the provided temporary directory or getImage() can return an image buffer.
    
    Parameters:
    file - the file to read
    tempDir - directory to store temporary files
    
    Throws:
    
    InvalidHeaderException - An exception that should be thrown if the header is invalid or cannot be read successfully.
    
    Exception - Anything else that might have gone wrong.
  - readHeader
```
void readHeader(URI uri,
              File tempDir)
                throws InvalidHeaderException,
                       Exception
```
    Reads the URI. The application expects that the image data is contiguous.
    
    Parameters:
    uri - the file to read
    tempDir - directory to store temporary files (only useful for local files)
    
    Throws:
    
    InvalidHeaderException - An exception that should be thrown if the header is invalid or cannot be read successfully.
    
    Exception - Anything else that might have gone wrong.
  - toString
```
String toString()
```
    Returns a formatted text representation of the image header (such as would be displayed in the 'Image Info' window).
    
    Overrides:
    
    toString in class Object
    
    Returns:
    image header as string
  - getSliceMetadata
```
String getSliceMetadata(int slice,
                      int seriesPoint)
```
    Returns a formatted text representation of the image header associated with the specified slice.
    
    Parameters:
    slice - the slice number
    seriesPoint - the series point
    
    Returns:
    image header as string
  - getSliceAnnotation
```
short[] getSliceAnnotation(int slice,
                         int seriesPoint)
```
    Returns a bitmap of annotation data associated with the specified slice.
    
    Parameters:
    slice - the slice number
    seriesPoint - the series point
    
    Returns:
    a bitmap

Interface ReadableHeader

Field Summary

Method Summary

Methods inherited from interface edu.uthscsa.ric.mango.MangoPluginType

Field Detail

ORIENTATION_CERTAINTY_HIGH

ORIENTATION_CERTAINTY_LOW

ORIENTATION_CERTAINTY_MID

Method Detail

getImage

getImageBuffers

getImageDescription

getImageDimensions

getImageFile

getImageRange

getImageType

getOrientation

getOrientationCertainty

getOrigin

getPreferredFileExtension

getPreviewImage

getTransforms

getVoxelDimensions

isThisFormat

readHeader

readHeader

toString

getSliceMetadata

getSliceAnnotation