ImageMetadata (SCIFIO Core 0.48.0 API)

All Superinterfaces:

HasMetaTable, org.scijava.Named

All Known Implementing Classes:

AbstractImageMetadata, DefaultImageMetadata
```
public interface ImageMetadata
extends org.scijava.Named, HasMetaTable
```
ImageMetadata stores the metadata for a single image within a dataset. Here, information common to every format (e.g. height, width, index information) can be stored and retrieved in a standard way.

Author:

Mark Hiner

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`void`	`addAxis(net.imagej.axis.AxisType axisType, long value)` As `addAxis(CalibratedAxis, long)` using the default calibration value, per `FormatTools.createAxis(AxisType)`.
`void`	`addAxis(net.imagej.axis.CalibratedAxis axis)` Appends the provided `CalibratedAxis` to the metadata's list of axes, with a length of 1.
`void`	`addAxis(net.imagej.axis.CalibratedAxis axis, long value)` Appends the provided CalibratedAxis to the current CalibratedAxis array and creates a corresponding entry with the specified value in axis lengths.
`ImageMetadata`	`copy()`
`void`	`copy(ImageMetadata toCopy)` Populates this ImageMetadata using the provided instance.
`List<net.imagej.axis.CalibratedAxis>`	`getAxes()` Returns an array of the types for axes associated with the specified image index.
`long[]`	`getAxesLengths()` Returns an array of the lengths for axes associated with the specified image index.
`long[]`	`getAxesLengths(List<net.imagej.axis.CalibratedAxis> axes)` Returns an array of the lengths for axes in the provided CalibratedAxis list.
`long[]`	`getAxesLengthsNonPlanar()` Returns an array of the lengths for the non-planar axes in this image.
`long[]`	`getAxesLengthsPlanar()` Returns an array of the lengths for the planar axes in this image.
`List<net.imagej.axis.CalibratedAxis>`	`getAxesNonPlanar()` Returns an array of the CalibratedAxis that define the number of planes in the dataset.
`List<net.imagej.axis.CalibratedAxis>`	`getAxesPlanar()` Returns an array of the CalibratedAxis that, together, define the bounds of a single plane in the dataset.
`net.imagej.axis.CalibratedAxis`	`getAxis(net.imagej.axis.AxisType axisType)` Returns the CalibratedAxis associated with the given type.
`net.imagej.axis.CalibratedAxis`	`getAxis(int axisIndex)` Gets the axis of the (zero-indexed) specified plane.
`int`	`getAxisIndex(net.imagej.axis.AxisType axisType)` As `getAxisIndex(CalibratedAxis)` but only requires the `AxisType` of the desired axis.
`int`	`getAxisIndex(net.imagej.axis.CalibratedAxis axis)` Returns the array index for the specified CalibratedAxis.
`long`	`getAxisLength(net.imagej.axis.AxisType t)` As `getAxisLength(CalibratedAxis)` but only requires the `AxisType` of the desired axis.
`long`	`getAxisLength(net.imagej.axis.CalibratedAxis t)` A convenience method for looking up the length of an axis based on its type.
`long`	`getAxisLength(int axisIndex)` Gets the length of the (zero-indexed) specified plane.
`int`	`getBitsPerPixel()` Returns the number of valid bits per pixel.
`int`	`getInterleavedAxisCount()` Returns the number of interleaved axes in this image.
`int`	`getPixelType()` Returns the data type associated with a pixel.
`int`	`getPlanarAxisCount()` Returns the number of planar axes in this image.
`long`	`getPlaneCount()`
`long`	`getPlaneSize()` Returns the size, in bytes, of one plane in this image.
`Object`	`getROIs()` Retrieves the ROIs associated with this image.
`long`	`getSize()` Returns the size, in bytes, of all planes in this image.
`Object`	`getTables()` Retrieves the tables associated with this image.
`long`	`getThumbSizeX()` Returns the width (in pixels) of the thumbnail planes in this image.
`long`	`getThumbSizeY()` Returns the height (in pixels) of the thumbnail planes in this image.
`boolean`	`isFalseColor()` Returns true if we can ignore the color map (if present).
`boolean`	`isIndexed()` Returns true if the planes are stored as indexed color.
`boolean`	`isLittleEndian()` Returns true if each pixel's bytes are in little endian order.
`boolean`	`isMetadataComplete()` Returns true if we are confident that all of the metadata stored within the image has been parsed.
`boolean`	`isMultichannel()` Returns true if the `Axes.CHANNEL` axis is a planar axis.
`boolean`	`isOrderCertain()` Returns true if we are confident that the dimension order is correct.
`boolean`	`isThumbnail()` Determines whether or not this image is a lower-resolution copy of another image.
`void`	`populate(String name, List<net.imagej.axis.CalibratedAxis> axes, long[] lengths, int pixelType, boolean orderCertain, boolean littleEndian, boolean indexed, boolean falseColor, boolean metadataComplete)` As `populate(String, List, long[], int, boolean, boolean, boolean, boolean, boolean)` but automatically determines bits per pixel.
`void`	`populate(String name, List<net.imagej.axis.CalibratedAxis> axes, long[] lengths, int pixelType, int bitsPerPixel, boolean orderCertain, boolean littleEndian, boolean indexed, boolean falseColor, boolean metadataComplete)` Convenience method for manually populating an ImageMetadata.
`void`	`setAxes(net.imagej.axis.CalibratedAxis... axes)` Sets the Axes types for this image.
`void`	`setAxes(net.imagej.axis.CalibratedAxis[] axes, long[] axisLengths)` Convenience method to set both the axis types and lengths for this ImageMetadata.
`void`	`setAxis(int index, net.imagej.axis.CalibratedAxis axis)` Sets the axis at the specified index, if an axis with a matching type is not already defined.
`void`	`setAxisLength(net.imagej.axis.AxisType axis, long length)` As `setAxisLength(CalibratedAxis, long)` but requires only the AxisType.
`void`	`setAxisLength(net.imagej.axis.CalibratedAxis axis, long length)` Sets the length for the specified axis.
`void`	`setAxisLengths(long[] axisLengths)` Sets the lengths of each axis.
`void`	`setAxisType(int index, net.imagej.axis.AxisType axis)` As `setAxis(int, CalibratedAxis)` but using the default calibration values, per `FormatTools.createAxis(AxisType)`.
`void`	`setAxisTypes(net.imagej.axis.AxisType... axisTypes)` Sets the Axes types for this image.
`void`	`setBitsPerPixel(int bitsPerPixel)` Sets the number of valid bits per pixel.
`void`	`setFalseColor(boolean falseColor)` Sets whether or not we can ignore the color map (if present).
`void`	`setIndexed(boolean indexed)` Sets whether or not the planes are stored as indexed color.
`void`	`setInterleavedAxisCount(int count)` Sets the number of interleaved axes in this image.
`void`	`setLittleEndian(boolean littleEndian)` Sets whether or not each pixel's bytes are in little endian order.
`void`	`setMetadataComplete(boolean metadataComplete)` Sets whether or not we are confident that all of the metadata stored within the image has been parsed.
`void`	`setOrderCertain(boolean orderCertain)` Sets whether or not we are confident that the dimension order is correct.
`void`	`setPixelType(int pixelType)` Sets the data type associated with a pixel.
`void`	`setPlanarAxisCount(int count)` Sets the number of planar axes in this image.
`void`	`setROIs(Object rois)` Sets the ROIs associated with this image.
`void`	`setTables(Object tables)` Sets the tables associated with this image.
`void`	`setThumbnail(boolean thumbnail)` Sets whether or not this image is a lower-resolution copy of another image.
`void`	`setThumbSizeX(long thumbSizeX)` Sets width (in pixels) of thumbnail planes in this image.
`void`	`setThumbSizeY(long thumbSizeY)` Sets height (in pixels) of thumbnail planes in this image.

Methods inherited from interface org.scijava.Named
getName, setName

Methods inherited from interface io.scif.HasMetaTable
getTable, setTable

- Method Detail
  - setThumbSizeX
```
void setThumbSizeX(long thumbSizeX)
```
    Sets width (in pixels) of thumbnail planes in this image.
  - setThumbSizeY
```
void setThumbSizeY(long thumbSizeY)
```
    Sets height (in pixels) of thumbnail planes in this image.
  - setPixelType
```
void setPixelType(int pixelType)
```
    Sets the data type associated with a pixel. Valid pixel type constants (e.g., FormatTools.INT8) are enumerated in FormatTools.
  - setBitsPerPixel
```
void setBitsPerPixel(int bitsPerPixel)
```
    Sets the number of valid bits per pixel.
  - setOrderCertain
```
void setOrderCertain(boolean orderCertain)
```
    Sets whether or not we are confident that the dimension order is correct.
  - setLittleEndian
```
void setLittleEndian(boolean littleEndian)
```
    Sets whether or not each pixel's bytes are in little endian order.
  - setIndexed
```
void setIndexed(boolean indexed)
```
    Sets whether or not the planes are stored as indexed color. An indexed color image treats each pixel value as an index into a color table containing one or more (typically 3) actual values for the pixel.
  - setPlanarAxisCount
```
void setPlanarAxisCount(int count)
```
    Sets the number of planar axes in this image. This value represents the number of dimensional axes constituting each Plane (as returned by the Reader.openPlane(int, long) methods). This value is necessary to determine the total plane count for an N-dimensional image, as well as how many pixels there are per plane.
    For example, suppose we have a 4-dimensional image with axes (X, Y, Z, T) and extents (768, 512, 7, 13). If there are two planar axes, then each plane is 768 x 512 and there are 7 x 13 = 91 total planes. But if we have three planar axes, then each plane is 768 x 512 x 7 and there are 13 total planes.
    
    See Also:
    
    Reader.openPlane(int, long)
  - setInterleavedAxisCount
```
void setInterleavedAxisCount(int count)
```
    Sets the number of interleaved axes in this image. This must be a value between [0, planarAxisCount). Interleaved axes are planar axes that do not constitute the "canonical" axes - e.g., in a CXY image with an interleaved axis count of 1, the C axis is interleaved, and each plane is an XY plane with C different representations.
  - setFalseColor
```
void setFalseColor(boolean falseColor)
```
    Sets whether or not we can ignore the color map (if present).
  - setMetadataComplete
```
void setMetadataComplete(boolean metadataComplete)
```
    Sets whether or not we are confident that all of the metadata stored within the image has been parsed.
  - setThumbnail
```
void setThumbnail(boolean thumbnail)
```
    Sets whether or not this image is a lower-resolution copy of another image.
  - setAxes
```
void setAxes(net.imagej.axis.CalibratedAxis[] axes,
             long[] axisLengths)
```
    Convenience method to set both the axis types and lengths for this ImageMetadata.
  - setAxisTypes
```
void setAxisTypes(net.imagej.axis.AxisType... axisTypes)
```
    Sets the Axes types for this image. Order is implied by ordering within this array
  - setAxes
```
void setAxes(net.imagej.axis.CalibratedAxis... axes)
```
    Sets the Axes types for this image. Order is implied by ordering within this array
  - setAxisLengths
```
void setAxisLengths(long[] axisLengths)
```
    Sets the lengths of each axis. Order is parallel of axes.
    NB: axes must already exist for this method to be called. Use setAxes(CalibratedAxis[]) or setAxes(net.imagej.axis.CalibratedAxis[], long[])
  - setAxisLength
```
void setAxisLength(net.imagej.axis.CalibratedAxis axis,
                   long length)
```
    Sets the length for the specified axis. Adds the axis if if its type is not already present in the image.
  - setAxisLength
```
void setAxisLength(net.imagej.axis.AxisType axis,
                   long length)
```
    As setAxisLength(CalibratedAxis, long) but requires only the AxisType.
  - setAxis
```
void setAxis(int index,
             net.imagej.axis.CalibratedAxis axis)
```
    Sets the axis at the specified index, if an axis with a matching type is not already defined. Otherwise the axes are re-ordered, per List.add(int, Object).
  - setAxisType
```
void setAxisType(int index,
                 net.imagej.axis.AxisType axis)
```
    As setAxis(int, CalibratedAxis) but using the default calibration values, per FormatTools.createAxis(AxisType).
  - setROIs
```
void setROIs(Object rois)
```
    Sets the ROIs associated with this image.
  - setTables
```
void setTables(Object tables)
```
    Sets the tables associated with this image.
  - getSize
```
long getSize()
```
    Returns the size, in bytes, of all planes in this image.
  - getPlaneSize
```
long getPlaneSize()
```
    Returns the size, in bytes, of one plane in this image.
  - getThumbSizeX
```
long getThumbSizeX()
```
    Returns the width (in pixels) of the thumbnail planes in this image.
  - getThumbSizeY
```
long getThumbSizeY()
```
    Returns the height (in pixels) of the thumbnail planes in this image.
  - getAxis
```
net.imagej.axis.CalibratedAxis getAxis(net.imagej.axis.AxisType axisType)
```
    Returns the CalibratedAxis associated with the given type. Useful to retrieve calibration information.
  - getPixelType
```
int getPixelType()
```
    Returns the data type associated with a pixel. Valid pixel type constants (e.g., FormatTools.INT8) are enumerated in FormatTools.
  - getBitsPerPixel
```
int getBitsPerPixel()
```
    Returns the number of valid bits per pixel.
  - isOrderCertain
```
boolean isOrderCertain()
```
    Returns true if we are confident that the dimension order is correct.
  - isLittleEndian
```
boolean isLittleEndian()
```
    Returns true if each pixel's bytes are in little endian order.
  - isIndexed
```
boolean isIndexed()
```
    Returns true if the planes are stored as indexed color.
  - getPlanarAxisCount
```
int getPlanarAxisCount()
```
    Returns the number of planar axes in this image.
  - getInterleavedAxisCount
```
int getInterleavedAxisCount()
```
    Returns the number of interleaved axes in this image.
  - isMultichannel
```
boolean isMultichannel()
```
    Returns true if the Axes.CHANNEL axis is a planar axis.
  - isFalseColor
```
boolean isFalseColor()
```
    Returns true if we can ignore the color map (if present).
  - isMetadataComplete
```
boolean isMetadataComplete()
```
    Returns true if we are confident that all of the metadata stored within the image has been parsed.
  - isThumbnail
```
boolean isThumbnail()
```
    Determines whether or not this image is a lower-resolution copy of another image.
    
    Returns:
    
    true if this image is a thumbnail
  - getAxis
```
net.imagej.axis.CalibratedAxis getAxis(int axisIndex)
```
    Gets the axis of the (zero-indexed) specified plane.
    
    Parameters:
    
    axisIndex - - index of the desired axis within this image
    
    Returns:
    
    Type of the desired plane.
  - getAxisLength
```
long getAxisLength(int axisIndex)
```
    Gets the length of the (zero-indexed) specified plane.
    
    Parameters:
    
    axisIndex - - index of the desired axis within this image
    
    Returns:
    
    Length of the desired axis, or 1 if the axis is not found.
  - getAxisLength
```
long getAxisLength(net.imagej.axis.CalibratedAxis t)
```
    A convenience method for looking up the length of an axis based on its type. No knowledge of plane ordering is necessary.
    
    Parameters:
    
    t - - CalibratedAxis to look up
    
    Returns:
    
    Length of axis t, or 1 if the axis is not found.
  - getAxisLength
```
long getAxisLength(net.imagej.axis.AxisType t)
```
    As getAxisLength(CalibratedAxis) but only requires the AxisType of the desired axis.
    
    Parameters:
    
    t - - CalibratedAxis to look up
    
    Returns:
    
    Length of axis t, or 1 if the axis is not found.
  - getAxisIndex
```
int getAxisIndex(net.imagej.axis.CalibratedAxis axis)
```
    Returns the array index for the specified CalibratedAxis. This index can be used in other Axes methods for looking up lengths, etc...
    This method can also be used as an existence check for the target CalibratedAxis.
    
    Parameters:
    
    axis - - axis to look up
    
    Returns:
    
    The index of the desired axis or -1 if not found.
  - getAxisIndex
```
int getAxisIndex(net.imagej.axis.AxisType axisType)
```
    As getAxisIndex(CalibratedAxis) but only requires the AxisType of the desired axis.
    
    Parameters:
    
    axisType - - axis type to look up
    
    Returns:
    
    The index of the desired axis or -1 if not found.
  - getAxes
```
List<net.imagej.axis.CalibratedAxis> getAxes()
```
    Returns an array of the types for axes associated with the specified image index. Order is consistent with the axis length (int) array returned by getAxesLengths().
    CalibratedAxis order is sorted and represents order within the image.
    
    Returns:
    
    List of CalibratedAxes. Ordering in the list indicates the axis order in the image.
  - getAxesPlanar
```
List<net.imagej.axis.CalibratedAxis> getAxesPlanar()
```
    Returns an array of the CalibratedAxis that, together, define the bounds of a single plane in the dataset.
    
    Returns:
    
    List of CalibratedAxes. Ordering in the list indicates the axis order in the image.
  - getAxesNonPlanar
```
List<net.imagej.axis.CalibratedAxis> getAxesNonPlanar()
```
    Returns an array of the CalibratedAxis that define the number of planes in the dataset.
    
    Returns:
    
    List of CalibratedAxes. Ordering in the list indicates the axis order in the image.
  - getPlaneCount
```
long getPlaneCount()
```
    Returns:
    
    the number of planes in this image
  - getAxesLengths
```
long[] getAxesLengths()
```
    Returns an array of the lengths for axes associated with the specified image index.
    Ordering is consistent with the CalibratedAxis array returned by getAxes().
    
    Returns:
    
    Sorted axis length array
  - getAxesLengths
```
long[] getAxesLengths(List<net.imagej.axis.CalibratedAxis> axes)
```
    Returns an array of the lengths for axes in the provided CalibratedAxis list.
    Ordering of the lengths is consistent with the provided ordering.
    
    Returns:
    
    Sorted axis length array
  - getAxesLengthsPlanar
```
long[] getAxesLengthsPlanar()
```
    Returns an array of the lengths for the planar axes in this image.
    
    Returns:
    
    Sorted axis length array
  - getAxesLengthsNonPlanar
```
long[] getAxesLengthsNonPlanar()
```
    Returns an array of the lengths for the non-planar axes in this image.
    
    Returns:
    
    Sorted axis length array
  - getROIs
```
Object getROIs()
```
    Retrieves the ROIs associated with this image.
  - getTables
```
Object getTables()
```
    Retrieves the tables associated with this image.
  - addAxis
```
void addAxis(net.imagej.axis.CalibratedAxis axis)
```
    Appends the provided CalibratedAxis to the metadata's list of axes, with a length of 1.
    
    Parameters:
    
    axis - - The new axis
  - addAxis
```
void addAxis(net.imagej.axis.CalibratedAxis axis,
             long value)
```
    Appends the provided CalibratedAxis to the current CalibratedAxis array and creates a corresponding entry with the specified value in axis lengths.
    
    Parameters:
    
    axis - - The new axis
    
    value - - length of the new axis
  - addAxis
```
void addAxis(net.imagej.axis.AxisType axisType,
             long value)
```
    As addAxis(CalibratedAxis, long) using the default calibration value, per FormatTools.createAxis(AxisType).
  - copy
```
ImageMetadata copy()
```
    Returns:
    
    A new copy of this ImageMetadata.
  - copy
```
void copy(ImageMetadata toCopy)
```
    Populates this ImageMetadata using the provided instance.
    
    Parameters:
    
    toCopy - - ImageMetadata to copy
  - populate
```
void populate(String name,
              List<net.imagej.axis.CalibratedAxis> axes,
              long[] lengths,
              int pixelType,
              boolean orderCertain,
              boolean littleEndian,
              boolean indexed,
              boolean falseColor,
              boolean metadataComplete)
```
    As populate(String, List, long[], int, boolean, boolean, boolean, boolean, boolean) but automatically determines bits per pixel.
  - populate
```
void populate(String name,
              List<net.imagej.axis.CalibratedAxis> axes,
              long[] lengths,
              int pixelType,
              int bitsPerPixel,
              boolean orderCertain,
              boolean littleEndian,
              boolean indexed,
              boolean falseColor,
              boolean metadataComplete)
```
    Convenience method for manually populating an ImageMetadata.

Interface ImageMetadata

Method Summary

Methods inherited from interface org.scijava.Named

Methods inherited from interface io.scif.HasMetaTable

Method Detail

setThumbSizeX

setThumbSizeY

setPixelType

setBitsPerPixel

setOrderCertain

setLittleEndian

setIndexed

setPlanarAxisCount

setInterleavedAxisCount

setFalseColor

setMetadataComplete

setThumbnail

setAxes

setAxisTypes

setAxes

setAxisLengths

setAxisLength

setAxisLength

setAxis

setAxisType

setROIs

setTables

getSize

getPlaneSize

getThumbSizeX

getThumbSizeY

getAxis

getPixelType

getBitsPerPixel

isOrderCertain

isLittleEndian

isIndexed

getPlanarAxisCount

getInterleavedAxisCount

isMultichannel

isFalseColor

isMetadataComplete

isThumbnail

getAxis

getAxisLength

getAxisLength

getAxisLength

getAxisIndex

getAxisIndex

getAxes

getAxesPlanar

getAxesNonPlanar

getPlaneCount

getAxesLengths

getAxesLengths

getAxesLengthsPlanar

getAxesLengthsNonPlanar

getROIs

getTables

addAxis

addAxis

addAxis

copy

copy

populate

populate