ImageVolume (Mango Plugin API)

```
public interface ImageVolume
```
ImageVolume is an interface that allows access to the image volume, with methods to get and put voxel values. It also provides access to the original header of the volume as ReadableHeader as well as some convenience methods to retrieve image and voxel dimensions.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`HEADER_FORMAT_ANALYZE`
`static String`	`HEADER_FORMAT_DES`
`static String`	`HEADER_FORMAT_DICOM_MR`
`static String`	`HEADER_FORMAT_DICOM_PET`
`static String`	`HEADER_FORMAT_DICOM_SC`
`static String`	`HEADER_FORMAT_NIFTI`
`static int`	`HEADER_TYPE_AVW` Deprecated.
`static int`	`HEADER_TYPE_NEMA` Deprecated.
`static int`	`HEADER_TYPE_NIFTI` Deprecated.
`static int`	`HEADER_TYPE_WRITABLE` Deprecated.

Method Summary

Methods
Modifier and Type	Method and Description
`long`	`convertIndexToOffset(int xLoc, int yLoc, int zLoc)` Converts an XYZ index into an array offset based on image orientation.
`Coordinate`	`getCenter()` Returns the center coordinate.
`int`	`getCurrentSeriesPoint()` Returns the current series point.
`ImageDescription`	`getImageDescription()` Returns the ImageDescription.
`ImageDimensions`	`getImageDimensions()` Returns the ImageDimensions.
`ImageRange`	`getImageRange()` Returns the ImageRange.
`ImageTransform`	`getImageTransform()` Returns the ImageTransform.
`ImageType`	`getImageType()` Returns the ImageType.
`String`	`getLabel(int seriesIndex)` Returns the series label for the specified index.
`long`	`getNativeIntegerValueAtIndex(int xLoc, int yLoc, int zLoc, int seriesIndex)` Returns the native integer value at a specified image index.
`String`	`getOrientationString()` Returns a string representation of this volume's data orientation (e.g., XYZ+--).
`Coordinate`	`getOrigin()` Returns the origin voxel location relative to the left-anterior-superior edge of the image.
`Coordinate`	`getOriginNativeOffsets()` Returns the original offsets.
`double`	`getRawVoxelValueAtIndex(int xLoc, int yLoc, int zLoc)` Returns the raw (without data scaling) voxel value at a specified image index.
`double`	`getRawVoxelValueAtIndex(int xLoc, int yLoc, int zLoc, int tLoc)` Returns the raw (without data scaling) voxel value at a specified image index and timepoint.
`double`	`getRawVoxelValueAtIndex(int xLoc, int yLoc, int zLoc, int tLoc, ImageTransform transform)` Returns the raw (without data scaling) voxel value at a specified image index and timepoint in transformed volume.
`double`	`getRawVoxelValueForOffset(long offset)` Returns the raw (without data scaling) voxel value at a specified offset.
`ReadableHeader`	`getReadableHeader()` Returns the ReadableHeader of this ImageVolume.
`int`	`getSeriesLength()` Returns the series length.
`double`	`getVolumeIntercept()` Returns the intercept value of the image [(0 - intercept) / scale] -- the value that should be on disk so that the screen value is 0.
`double`	`getVolumeInterceptScreen()` Returns the intercept value of the image [(intercept) / scale] -- if the value on disk is 0, this is the screen value.
`VoxelDimensions`	`getVoxelDimensions()` Returns the VoxelDimensions.
`double`	`getVoxelValueAtCoordinate(double xLoc, double yLoc, double zLoc)` Returns the voxel value at a specified coordinate in real world space.
`double`	`getVoxelValueAtCoordinate(double xLoc, double yLoc, double zLoc, int tLoc)` Returns the voxel value at a specified coordinate and timepoint in real world space.
`double`	`getVoxelValueAtCoordinate(double xLoc, double yLoc, double zLoc, int tLoc, ImageTransform transform)` Returns the voxel value at a specified coordinate and timepoint in a transformed world space.
`double`	`getVoxelValueAtIndex(int xLoc, int yLoc, int zLoc)` Returns the voxel value at a specified image index.
`double`	`getVoxelValueAtIndex(int xLoc, int yLoc, int zLoc, int tLoc)` Returns the voxel value at a specified image index and timepoint.
`double`	`getVoxelValueAtIndex(int xLoc, int yLoc, int zLoc, int tLoc, ImageTransform transform)` Returns the voxel value at a specified image index and timepoint in transformed volume.
`double`	`getVoxelValueForOffset(long offset)` Returns the voxel value at a specified offset.
`ByteBuffer`	`getWorkBuffer()` Deprecated.
`ByteBuffer[]`	`getWorkBuffers()` Returns the work buffer (a float buffer), for use with advanced methods.
`int`	`getXDim()` Returns x image dimension.
`double`	`getXSize()` Returns x voxel size.
`int`	`getYDim()` Returns y image dimension.
`double`	`getYSize()` Returns y voxel size.
`int`	`getZDim()` Returns z image dimension.
`double`	`getZSize()` Returns z voxel size.
`void`	`putVoxelValueAtCoordinate(double xLoc, double yLoc, double zLoc, double value)` Deprecated.
`void`	`putVoxelValueAtCoordinate(double xLoc, double yLoc, double zLoc, int tLoc, double value)` Deprecated.
`void`	`putVoxelValueAtCoordinate(double xLoc, double yLoc, double zLoc, int tLoc, double value, ImageTransform transform)` Deprecated.
`void`	`putVoxelValueAtIndex(int xLoc, int yLoc, int zLoc, double value)` Replaces a voxel value at a specified image index.
`void`	`putVoxelValueAtIndex(int xLoc, int yLoc, int zLoc, int tLoc, double value)` Replaces a voxel value at a specified image index and timepoint.
`void`	`putVoxelValueAtIndex(int xLoc, int yLoc, int zLoc, int tLoc, double value, ImageTransform transform)` Deprecated.
`void`	`putVoxelValueAtOffset(int offset, double value)` Replaces a voxel value at a specified offset.
`File`	`readFiles(File file)` Deprecated.
`URI`	`readFiles(URI file)` Reads a file into an ImageVolume.
`URI`	`readFiles(URI file, boolean readOnly)` Reads a file into an ImageVolume.
`void`	`setCurrentSeriesPoint(int point)` Sets the current series point.
`void`	`setForceLoadInThead(boolean forceLoadInThread)` Set to true to force loading this image in the current thread, instead of a background thread.
`void`	`setImageAsDirty()` Flag the image as dirty (needs to be saved).
`void`	`setOrigin(Coordinate origin)` Sets the origin of this ImageVolume.
`void`	`setReadOnly(boolean readOnly)` Set this image as read-only.
`String`	`toString()` Returns a string representation of this ImageVolume.
`void`	`volumeOperationCompleted()` Notifies volume that an image operation has been performed.
`void`	`volumeOperationCompleted(String des)` Notifies volume that an image operation has been performed.
`void`	`writeFilesAs(File headerFile, int headerType, String otherFormatName, ImageType it, boolean applyDataScales, boolean fitPrecision)` Deprecated.
`void`	`writeFilesAs(File headerFile, String formatName, ImageType it, String orientation, boolean applyDataScales, boolean fitPrecision)` Write file.

- Field Detail
  - HEADER_TYPE_AVW
```
@Deprecated
static final int HEADER_TYPE_AVW
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - HEADER_TYPE_NEMA
```
@Deprecated
static final int HEADER_TYPE_NEMA
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - HEADER_TYPE_NIFTI
```
@Deprecated
static final int HEADER_TYPE_NIFTI
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - HEADER_TYPE_WRITABLE
```
@Deprecated
static final int HEADER_TYPE_WRITABLE
```
    Deprecated.
    
    See Also:
    Constant Field Values
  - HEADER_FORMAT_ANALYZE
```
static final String HEADER_FORMAT_ANALYZE
```
    See Also:
    Constant Field Values
  - HEADER_FORMAT_DES
```
static final String HEADER_FORMAT_DES
```
    See Also:
    Constant Field Values
  - HEADER_FORMAT_DICOM_MR
```
static final String HEADER_FORMAT_DICOM_MR
```
    See Also:
    Constant Field Values
  - HEADER_FORMAT_DICOM_PET
```
static final String HEADER_FORMAT_DICOM_PET
```
    See Also:
    Constant Field Values
  - HEADER_FORMAT_DICOM_SC
```
static final String HEADER_FORMAT_DICOM_SC
```
    See Also:
    Constant Field Values
  - HEADER_FORMAT_NIFTI
```
static final String HEADER_FORMAT_NIFTI
```
    See Also:
    Constant Field Values
- Method Detail
  - convertIndexToOffset
```
long convertIndexToOffset(int xLoc,
                        int yLoc,
                        int zLoc)
```
    Converts an XYZ index into an array offset based on image orientation.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    
    Returns:
    image offset
  - getCenter
```
Coordinate getCenter()
```
    Returns the center coordinate.
    
    Returns:
    the center coordinate
  - getCurrentSeriesPoint
```
int getCurrentSeriesPoint()
```
    Returns the current series point.
    
    Returns:
    the current series point
  - getImageDescription
```
ImageDescription getImageDescription()
```
    Returns the ImageDescription.
    
    Returns:
    the ImageDescription
  - getImageDimensions
```
ImageDimensions getImageDimensions()
```
    Returns the ImageDimensions.
    
    Returns:
    the ImageDimensions
  - getImageRange
```
ImageRange getImageRange()
```
    Returns the ImageRange.
    
    Returns:
    the ImageRange
  - getImageTransform
```
ImageTransform getImageTransform()
```
    Returns the ImageTransform.
    
    Returns:
    the ImageTransform
  - getImageType
```
ImageType getImageType()
```
    Returns the ImageType.
    
    Returns:
    the ImageType
  - getLabel
```
String getLabel(int seriesIndex)
```
    Returns the series label for the specified index.
    
    Parameters:
    seriesIndex - the series index
    
    Returns:
    the series label
  - getNativeIntegerValueAtIndex
```
long getNativeIntegerValueAtIndex(int xLoc,
                                int yLoc,
                                int zLoc,
                                int seriesIndex)
```
    Returns the native integer value at a specified image index. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    seriesIndex - series index
    
    Returns:
    integer value at specified image index
  - getOrientationString
```
String getOrientationString()
```
    Returns a string representation of this volume's data orientation (e.g., XYZ+--).
    
    Returns:
    a string representation of this volume's data orientation
  - getOrigin
```
Coordinate getOrigin()
```
    Returns the origin voxel location relative to the left-anterior-superior edge of the image.
    
    Returns:
    the origin as a Coordinate
  - getOriginNativeOffsets
```
Coordinate getOriginNativeOffsets()
```
    Returns the original offsets.
    
    Returns:
    the offests as a Coordinate
  - getRawVoxelValueAtIndex
```
double getRawVoxelValueAtIndex(int xLoc,
                             int yLoc,
                             int zLoc)
```
    Returns the raw (without data scaling) voxel value at a specified image index. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    
    Returns:
    value at specified image index
  - getRawVoxelValueAtIndex
```
double getRawVoxelValueAtIndex(int xLoc,
                             int yLoc,
                             int zLoc,
                             int tLoc)
```
    Returns the raw (without data scaling) voxel value at a specified image index and timepoint. An index of (0, 0, 0) corresponds to the LAS corner..
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    
    Returns:
    value at specified image index and timepoint
  - getRawVoxelValueAtIndex
```
double getRawVoxelValueAtIndex(int xLoc,
                             int yLoc,
                             int zLoc,
                             int tLoc,
                             ImageTransform transform)
```
    Returns the raw (without data scaling) voxel value at a specified image index and timepoint in transformed volume. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    transform - image transform to use.
    
    Returns:
    value at a specified image index and timepoint in transformed volume
  - getRawVoxelValueForOffset
```
double getRawVoxelValueForOffset(long offset)
```
    Returns the raw (without data scaling) voxel value at a specified offset. The offset refers to the offset into the data array as it is arranged on disk.
    
    Parameters:
    offset - image array offset
    
    Returns:
    value at specified offset
  - getReadableHeader
```
ReadableHeader getReadableHeader()
```
    Returns the ReadableHeader of this ImageVolume.
    
    Returns:
    the ReadableHeader of this ImageVolume
  - getSeriesLength
```
int getSeriesLength()
```
    Returns the series length.
    
    Returns:
    the series length
  - getVolumeIntercept
```
double getVolumeIntercept()
```
    Returns the intercept value of the image [(0 - intercept) / scale] -- the value that should be on disk so that the screen value is 0.
    
    Returns:
    the intercept value of the image
  - getVolumeInterceptScreen
```
double getVolumeInterceptScreen()
```
    Returns the intercept value of the image [(intercept) / scale] -- if the value on disk is 0, this is the screen value.
    
    Returns:
    the intercept value of the image
  - getVoxelDimensions
```
VoxelDimensions getVoxelDimensions()
```
    Returns the VoxelDimensions.
    
    Returns:
    the VoxelDimensions
  - getVoxelValueAtCoordinate
```
double getVoxelValueAtCoordinate(double xLoc,
                               double yLoc,
                               double zLoc)
```
    Returns the voxel value at a specified coordinate in real world space.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    
    Returns:
    value at specified world space coordinate
  - getVoxelValueAtCoordinate
```
double getVoxelValueAtCoordinate(double xLoc,
                               double yLoc,
                               double zLoc,
                               int tLoc)
```
    Returns the voxel value at a specified coordinate and timepoint in real world space.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    
    Returns:
    value at specified world space coordinate and timepoint
  - getVoxelValueAtCoordinate
```
double getVoxelValueAtCoordinate(double xLoc,
                               double yLoc,
                               double zLoc,
                               int tLoc,
                               ImageTransform transform)
```
    Returns the voxel value at a specified coordinate and timepoint in a transformed world space.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    transform - world space transform to use.
    
    Returns:
    value at a specified coordinate and timepoint in a transformed world space
  - getVoxelValueAtIndex
```
double getVoxelValueAtIndex(int xLoc,
                          int yLoc,
                          int zLoc)
```
    Returns the voxel value at a specified image index. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    
    Returns:
    value at specified image index
  - getVoxelValueAtIndex
```
double getVoxelValueAtIndex(int xLoc,
                          int yLoc,
                          int zLoc,
                          int tLoc)
```
    Returns the voxel value at a specified image index and timepoint. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    
    Returns:
    value at specified image index and timepoint
  - getVoxelValueAtIndex
```
double getVoxelValueAtIndex(int xLoc,
                          int yLoc,
                          int zLoc,
                          int tLoc,
                          ImageTransform transform)
```
    Returns the voxel value at a specified image index and timepoint in transformed volume. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    transform - transform to apply to the image
    
    Returns:
    value at a specified image index and timepoint in transformed volume
  - getVoxelValueForOffset
```
double getVoxelValueForOffset(long offset)
```
    Returns the voxel value at a specified offset. The offset refers to the offset into the data array as it is arranged on disk.
    
    Parameters:
    offset - image array offset
    
    Returns:
    value at specified offset
  - getWorkBuffer
```
@Deprecated
ByteBuffer getWorkBuffer()
```
    Deprecated.
    
    Returns the work buffer (a float buffer), for use with advanced methods. Buffer data is stored in the image's natural data order. The method convertIndexToOffset() can be used to access the buffer using XYZ coordinates. Buffer data does not include data scales; it stores raw data values.
    
    Data scales can be fetched from ImageRange using getDataScaleSlopes() and getDataScaleIntercepts().
    The data scale index can be calculated as (offset / (numRows * numCols)). The number of rows and columns can be gotten from ImageDimensions. If you know that the data scales are global (e.g., see hasGlobalDataScaleSlope()), than it would be unnecessary to use the array and index method.
    
    The method getRawVoxelValueAtOffset(offset) will give the same result as getWorkBuffer().getFloat(offset * 4).
    
    The method getVoxelValueAtOffset(offset) will give the same result as (getWorkBuffer().getFloat(offset * 4) * dataScaleSlope[dataScaleIndex]) + dataScaleIntercept[dataScaleIndex].
    
    Returns:
    image work buffer
  - getWorkBuffers
```
ByteBuffer[] getWorkBuffers()
```
    Returns the work buffer (a float buffer), for use with advanced methods. Buffer data is stored in the image's natural data order. The method convertIndexToOffset() can be used to access the buffer using XYZ coordinates. Buffer data does not include data scales; it stores raw data values.
    
    Data scales can be fetched from ImageRange using getDataScaleSlopes() and getDataScaleIntercepts().
    The data scale index can be calculated as (offset / (numRows * numCols)). The number of rows and columns can be gotten from ImageDimensions. If you know that the data scales are global (e.g., see hasGlobalDataScaleSlope()), than it would be unnecessary to use the array and index method.
    
    The method getRawVoxelValueAtOffset(offset) will give the same result as getWorkBuffer().getFloat(offset * 4).
    
    The method getVoxelValueAtOffset(offset) will give the same result as (getWorkBuffer().getFloat(offset * 4) * dataScaleSlope[dataScaleIndex]) + dataScaleIntercept[dataScaleIndex].
    
    Returns:
    image work buffer
  - getXDim
```
int getXDim()
```
    Returns x image dimension.
    
    Returns:
    x image dimension
  - getXSize
```
double getXSize()
```
    Returns x voxel size.
    
    Returns:
    x voxel size
  - getYDim
```
int getYDim()
```
    Returns y image dimension.
    
    Returns:
    y image dimension
  - getYSize
```
double getYSize()
```
    Returns y voxel size.
    
    Returns:
    y voxel size
  - getZDim
```
int getZDim()
```
    Returns z image dimension.
    
    Returns:
    z image dimension
  - getZSize
```
double getZSize()
```
    Returns z voxel size.
    
    Returns:
    z voxel size
  - putVoxelValueAtCoordinate
```
@Deprecated
void putVoxelValueAtCoordinate(double xLoc,
                                        double yLoc,
                                        double zLoc,
                                        double value)
```
    Deprecated.
    
    Replaces a voxel value at a specified coordinate in real world space.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    value - replacement value
  - putVoxelValueAtCoordinate
```
@Deprecated
void putVoxelValueAtCoordinate(double xLoc,
                                        double yLoc,
                                        double zLoc,
                                        int tLoc,
                                        double value)
```
    Deprecated.
    
    Replaces a voxel value at a specified coordinate and timepoint in real world space.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    value - replacement value
  - putVoxelValueAtCoordinate
```
@Deprecated
void putVoxelValueAtCoordinate(double xLoc,
                                        double yLoc,
                                        double zLoc,
                                        int tLoc,
                                        double value,
                                        ImageTransform transform)
```
    Deprecated.
    
    Replaces a voxel value at a specified coordinate and timepoint in transformed world space.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    transform - world space transform to use
    value - replacement value
  - putVoxelValueAtIndex
```
void putVoxelValueAtIndex(int xLoc,
                        int yLoc,
                        int zLoc,
                        double value)
```
    Replaces a voxel value at a specified image index. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    value - replacement value
  - putVoxelValueAtIndex
```
void putVoxelValueAtIndex(int xLoc,
                        int yLoc,
                        int zLoc,
                        int tLoc,
                        double value)
```
    Replaces a voxel value at a specified image index and timepoint. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    value - replacement value
  - putVoxelValueAtIndex
```
@Deprecated
void putVoxelValueAtIndex(int xLoc,
                                   int yLoc,
                                   int zLoc,
                                   int tLoc,
                                   double value,
                                   ImageTransform transform)
```
    Deprecated.
    
    Replaces a voxel value at a specified image index and timepoint in transformed volume. An index of (0, 0, 0) corresponds to the LAS corner.
    
    Parameters:
    xLoc - X index
    yLoc - Y index
    zLoc - Z index
    tLoc - timepoint
    value - replacement value
    transform - image transform to use
  - putVoxelValueAtOffset
```
void putVoxelValueAtOffset(int offset,
                         double value)
```
    Replaces a voxel value at a specified offset.
    
    Parameters:
    offset - image array offset
    value - replacement value
  - readFiles
```
@Deprecated
File readFiles(File file)
               throws InvalidHeaderException,
                      Exception
```
    Deprecated.
    
    Reads a file into an ImageVolume.
    
    Parameters:
    file - a file to read
    
    Returns:
    the header file that was found (could be same as parameter)
    
    Throws:
    
    InvalidHeaderException - invalid header exception
    
    Exception - exception
  - readFiles
```
URI readFiles(URI file)
              throws InvalidHeaderException,
                     Exception
```
    Reads a file into an ImageVolume.
    
    Parameters:
    file - a file to read
    
    Returns:
    the header file that was found (could be same as parameter)
    
    Throws:
    
    InvalidHeaderException - invalid header exception
    
    Exception - exception
  - readFiles
```
URI readFiles(URI file,
            boolean readOnly)
              throws InvalidHeaderException,
                     Exception
```
    Reads a file into an ImageVolume.
    
    Parameters:
    file - a file to read
    readOnly - true to load in read-only mode (will use less memory if datatype is byte or short)
    
    Returns:
    the header file that was found (could be same as parameter)
    
    Throws:
    
    InvalidHeaderException - invalid header exception
    
    Exception - exception
  - setCurrentSeriesPoint
```
void setCurrentSeriesPoint(int point)
```
    Sets the current series point.
    
    Parameters:
    point - the current series point
  - setForceLoadInThead
```
void setForceLoadInThead(boolean forceLoadInThread)
```
    Set to true to force loading this image in the current thread, instead of a background thread.
    
    Parameters:
    forceLoadInThread - true to force loading this image in the current thread, false otherwise
  - setImageAsDirty
```
void setImageAsDirty()
```
    Flag the image as dirty (needs to be saved).
  - setOrigin
```
void setOrigin(Coordinate origin)
```
    Sets the origin of this ImageVolume.
    
    Parameters:
    origin - the new origin
  - setReadOnly
```
void setReadOnly(boolean readOnly)
```
    Set this image as read-only. This flag is only applicable to integer images. When true, the backing data store will use the native bit depth of the image, which may be less than the default 4-byte floating point backing data store. To access read-only data use getNativeIntegerValueAtIndex().
    
    Parameters:
    readOnly - true to set image as read-only, false otherwise
  - toString
```
String toString()
```
    Returns a string representation of this ImageVolume.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    a string representation
  - volumeOperationCompleted
```
void volumeOperationCompleted()
```
    Notifies volume that an image operation has been performed.
  - volumeOperationCompleted
```
void volumeOperationCompleted(String des)
```
    Notifies volume that an image operation has been performed.
    
    Parameters:
    des - a short description of the operation
  - writeFilesAs
```
@Deprecated
void writeFilesAs(File headerFile,
                           int headerType,
                           String otherFormatName,
                           ImageType it,
                           boolean applyDataScales,
                           boolean fitPrecision)
                  throws Exception
```
    Deprecated.
    
    Write file.
    
    Parameters:
    headerFile - file to save
    headerType - header type (see header type constants such as ImageVolume.HEADER_TYPE_NIFTI)
    otherFormatName - if headerType is ImageVolume.HEADER_TYPE_WRITABLE, then otherFormatName must equal a loaded WritableHeader plugin name
    it - the ImageType of the output image
    applyDataScales - true to multiply data scales into the image, false to leave data scale information in header
    fitPrecision - true to fit the image data range to the data type range, false otherwise
    
    Throws:
    
    Exception - exception
  - writeFilesAs
```
void writeFilesAs(File headerFile,
                String formatName,
                ImageType it,
                String orientation,
                boolean applyDataScales,
                boolean fitPrecision)
                  throws Exception
```
    Write file.
    
    Parameters:
    headerFile - file to save
    formatName - string representation of header format (e.g., HEADER_FORMAT_NIFTI)
    it - the ImageType of the output image
    orientation - the orientation string (e.g., "XYZ+++") or null to use current
    applyDataScales - true to multiply data scales into the image, false to leave data scale information in header
    fitPrecision - true to fit the image data range to the data type range, false otherwise
    
    Throws:
    
    Exception - exception

Interface ImageVolume

Field Summary

Method Summary

Field Detail

HEADER_TYPE_AVW

HEADER_TYPE_NEMA

HEADER_TYPE_NIFTI

HEADER_TYPE_WRITABLE

HEADER_FORMAT_ANALYZE

HEADER_FORMAT_DES

HEADER_FORMAT_DICOM_MR

HEADER_FORMAT_DICOM_PET

HEADER_FORMAT_DICOM_SC

HEADER_FORMAT_NIFTI

Method Detail

convertIndexToOffset

getCenter

getCurrentSeriesPoint

getImageDescription

getImageDimensions

getImageRange

getImageTransform

getImageType

getLabel

getNativeIntegerValueAtIndex

getOrientationString

getOrigin

getOriginNativeOffsets

getRawVoxelValueAtIndex

getRawVoxelValueAtIndex

getRawVoxelValueAtIndex

getRawVoxelValueForOffset

getReadableHeader

getSeriesLength

getVolumeIntercept

getVolumeInterceptScreen

getVoxelDimensions

getVoxelValueAtCoordinate

getVoxelValueAtCoordinate

getVoxelValueAtCoordinate

getVoxelValueAtIndex

getVoxelValueAtIndex

getVoxelValueAtIndex

getVoxelValueForOffset

getWorkBuffer

getWorkBuffers

getXDim

getXSize

getYDim

getYSize

getZDim

getZSize

putVoxelValueAtCoordinate

putVoxelValueAtCoordinate

putVoxelValueAtCoordinate

putVoxelValueAtIndex

putVoxelValueAtIndex

putVoxelValueAtIndex

putVoxelValueAtOffset

readFiles

readFiles

readFiles

setCurrentSeriesPoint

setForceLoadInThead

setImageAsDirty

setOrigin

setReadOnly

toString

volumeOperationCompleted

volumeOperationCompleted

writeFilesAs

writeFilesAs