java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FileNRRD

```
public class FileNRRD
extends FileBase
```
See Also:

FileIO, FileInfoNRRD, FileRaw

Field Summary

Fields
Modifier and Type	Field	Description
`private boolean`	`apInvert`	True for RAS and LAS, false for LPS.
`private boolean`	`autoSequence`	True if data file: [] encountered If true, autosequence using integer format specification varied according to , , and .
`private double[]`	`axisMaxs`	Maximum axis value.
`private double[]`	`axisMins`	Minimum axis value.
`private int[]`	`axisOrientation`	For each axis R2L, L2R, A2P, P2A, I2S, or S2I
`private java.lang.String`	`baseAfterNumber`	In autosequencing number between a capital D and the last period used in generating filenames.
`private java.lang.String`	`baseBeforeNumber`	In autosequencing number before percentage sign and period used in generating start of autosequenced filename.
`private boolean`	`baseNumber`	Used if autosequencing.
`private static int`	`CELL`	The location of the sample is located in the interior of the grid element.
`private int[]`	`centers`	May remain null or may be created as NONE, CELL, or NODE.
`private java.lang.String[][]`	`dwmriGradient`	"modality:=DWMRI" : This key/value pair explicitly indicates that the image is a diffusion-weighted MRI scan, and it implies that all of the following key/value pairs are also set in the header: "DWMRI_b-value:=b " : This key/value pair gives the (scalar) diffusion-weighting value, in units of s/mm^2.
`private java.lang.String[][]`	`dwmriNex`	"DWMRI_NEX_NNNN:=M " means that the information provided for image NNNN (either gradient or B-matrix) is the same as for image NNNN+1, NNNN+2, up to and including NNNN+M-1.
`private boolean`	`endianess`	DOCUMENT ME!
`private java.lang.String`	`ext`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoNRRD`	`fileInfo`	DOCUMENT ME!
`private FileInfoNRRD`	`fileInfoSub`	DOCUMENT ME!
`private long`	`fileLength`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private boolean`	`fileNameSequence`	DOCUMENT ME!
`private java.lang.String[]`	`fileNameSet`	DOCUMENT ME!
`private int`	`fileNumber`	DOCUMENT ME!
`private int[]`	`finishBlank`	DOCUMENT ME!
`private int[]`	`finishQuote`	DOCUMENT ME!
`private boolean`	`foundEOF`	DOCUMENT ME!
`private boolean`	`foundEOHeader`	DOCUMENT ME!
`private boolean`	`gunzip`	If true, data has gzip compression.
`private ModelImage`	`image`	DOCUMENT ME!
`private int[]`	`imgExtents`	DOCUMENT ME!
`private java.lang.String[]`	`kindsString`	Kind of information represented by the samples along each axis.
`private static int`	`LPS`	A patient-based right-handed coordinate frame, with ordered basis vectors pointing towards left, posterior, and superior, respectively.
`private static int`	`LPST`	Like LPS, but with time along the fourth axis.
`private TransMatrix`	`matrix`	DOCUMENT ME!
`private double[][]`	`measurementFrame`	The measurement frame is a basic (per-array) field specification (not per-axis), which identifies a spaceDim-by-spaceDim matrix, where spaceDim is the dimension of the word space (implied by space or given by space dimension).
`private int`	`mipavDataType`	DOCUMENT ME!
`private int`	`mipavDimensions`	DOCUMENT ME!
`private java.lang.String[]`	`mipavLabels`	MIPAV axis names such as X, Y, or Z
`private int[]`	`mipavUnits`	DOCUMENT ME!
`private static int`	`NODE`	The location of the sample is at the boundary between grid elements.
`private static int`	`NONE`	Centering information for this axis is either meaningless or unknown.
`private int`	`nrrdDataType`	Does not tell if color or black and white.
`private int`	`nrrdDimensions`	May not be the same as MIPAV dimensions because in nrrd color is a dimension.
`private java.lang.String[]`	`nrrdLabels`	nrrd axis names such as X, Y, or Z
`private int[]`	`nrrdSizes`	The number of samples along each nrrd axis
`private java.lang.String[]`	`nrrdSpaceUnits`	DOCUMENT ME!
`private java.lang.String[]`	`nrrdUnits`	Units of measurement of nrrd axis
`private int`	`numColors`	DOCUMENT ME!
`private int`	`numSpaceKinds`	Number of nrrd dimensions for which the kinds string equals "SPACE".
`private int`	`numThicknesses`	Number of axes for which thicknesses values found
`private long`	`offset1`	DOCUMENT ME!
`private boolean`	`oneFile`	If true, header and data both stored in .nrrd file.
`private boolean`	`oneFileStorage`	True for .nrrd file with header and data in the same file.
`private float[]`	`origin`	DOCUMENT ME!
`private int`	`paddingNumber`	In autosequencing if the sequence number length is less than the padding number, zeroes are added to the front of the sequence number until the sequence number length equals the padding number.
`private int`	`planarConfig`	0 indicates pixels are RGB, RGB chunky 1 indicates pixels are RRR, GGG, BBB planar.
`private boolean`	`reorder`	The orientation information in some NRRD files cannot be applied to MIPAV without dimension reordering.
`private float[]`	`resols`	DOCUMENT ME!
`private boolean`	`RGBAOrder`	If true, data is a specialized form of 4-color with red, green, blue, and alpha, in that order.
`private boolean`	`rlInvert`	True for RAS.
`private static int`	`SCANNER_XYZ`	A scanner-based right-handed coordinate frame, used in ACR/NEMA 2.0.
`private static int`	`SCANNER_XYZ_TIME`	Like SCANNER_XYZ, but with time along the fourth axis.
`private int`	`sequenceFinish`	DOCUMENT ME!
`private int`	`sequenceStart`	DOCUMENT ME!
`private int`	`sequenceStep`	DOCUMENT ME!
`private int`	`skippedBytes`	Number of bytes to skip
`private int`	`skippedLines`	Number of lines to skip
`private float`	`sliceThickness`	DOCUMENT ME!
`private int`	`space`	RAS, LAS, LPS, RAST, LAST, LPST, SCANNER_XYZ, SCANNER_XYZ_TIME, THREED_RIGHT_HANDED, THREED_LEFT_HANDED, THREED_RIGHT_HANDED_TIME, or THREED_LEFT_HANDED_TIME
`private double[][]`	`spaceDirections`	Second index of spaceDirections specifies row of matrix to set.
`private double[]`	`spaceOrigin`	Used to set origin values.
`private java.lang.String`	`spaceUnitsString`	DOCUMENT ME!
`private double[]`	`spacings`	Resolutions values for nrrd axes
`private int[]`	`startBlank`	DOCUMENT ME!
`private int[]`	`startQuote`	DOCUMENT ME!
`private int`	`subdim`	DOCUMENT ME!
`private double[]`	`thicknesses`	Used to obtain MIPAV sliceThickness value
`private static int`	`THREED_LEFT_HANDED`	Any left-handed three-dimensional space.
`private static int`	`THREED_LEFT_HANDED_TIME`	Like THREEE_LEFT_HANDED, but with time along the fourth axis.
`private static int`	`THREED_RIGHT_HANDED`	Any right-handed three-dimensional space.
`private static int`	`THREED_RIGHT_HANDED_TIME`	Like THREED_RIGHT_HANDED, but with time along the fourth axis.
`private static int`	`UNKNOWN`	DOCUMENT ME!
`private float`	`versionNumber`	Version of the NRRD file format being used.
`private static int`	`writeVersionNumber`	version number of NRRD for writing

Fields inherited from class gov.nih.mipav.model.file.FileBase
BIG_ENDIAN, bitsPerPixel, fileNames, LITTLE_ENDIAN, pBarVisible, raFile, READ, READ_WRITE

Constructor Summary

Constructors
Constructor Description

FileNRRD(java.lang.String fName, java.lang.String fDir)
Constructs new file object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`private int[]`	`getAxisOrientation(TransMatrix mat)`	Return the 3 axis orientation codes that correspond to the closest standard anatomical orientation of the (i,j,k) axes.
`FileInfoNRRD`	`getFileInfo()`	Returns the FileInfoNRRD read from the file.
`private int`	`getOffset(FileInfoNRRD fileInfo)`	Helper method to calculate the offset for getting only the middle NRRD image slice from the 3D file.
`boolean`	`readHeader(java.lang.String imageFileName, java.lang.String fileDir)`	Reads the NRRD header and stores the information in fileInfo.
`ModelImage`	`readImage(boolean one, boolean doHeader)`	Reads a NRRD image file by reading the header then making a FileRaw to read the image for all filenames in the file list.
`private java.lang.String`	`readLine()`	Reads lines of the file and strips comments indicated by the # symbol until a nonnull String results or the end of the file is reached or a blank line containing end of header with zero characters is reached.
`void`	`setFileInfo(FileInfoNRRD fileInfo)`
`private void`	`setFileInfo(FileInfoNRRD fileInfo, ModelImage image)`	DOCUMENT ME!
`private void`	`updateorigins(FileInfoBase[] fileInfo)`	Updates the start locations.
`private boolean`	`writeHeader(ModelImage image, java.lang.String fhName, java.lang.String fDir, int beginSlice, int endSlice, int beginTime, int endTime)`	write NRRD header
`private void`	`writeHeader3DTo2D(ModelImage img, java.lang.String headerName, java.lang.String headerDir, FileWriteOptions options)`	Method to save off the header from a 3D image into 2D header files sequentially named (similar to the method in FileRaw).
`private void`	`writeHeader4DTo3D(ModelImage image, java.lang.String fileName, java.lang.String fileDir, FileWriteOptions options)`	This method is used when saving a 4D image in an array of 3D files.
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes a NRRD format type image.

Methods inherited from class gov.nih.mipav.model.file.FileBase
addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, floatToBytes, getBufferDouble, getBufferFloat, getBufferInt, getBufferLong, getBufferShort, getBufferUShort, getDataType, getDouble, getFloat, getInt, getLong, getProgressChangeListeners, getRaFile, getSignedShort, getString, getUInt, getUnsignedByte, getUnsignedShort, intToBytes, isBigEndian, isProgressBarVisible, linkProgress, longToBytes, readDouble, readFloat, readInt, readLong, readShort, readString, readUnsignedShort, removeProgressChangeListener, setBigEndian, setBufferFloat, setBufferInt, setBufferLong, setBufferShort, setBufferString, setDataType, setEndianess, shortToBytes, writeBytes, writeDouble, writeFloat, writeInt, writeLong, writeShort

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

- Field Detail
  - UNKNOWN
```
private static final int UNKNOWN
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - LPS
```
private static final int LPS
```
    A patient-based right-handed coordinate frame, with ordered basis vectors pointing towards left, posterior, and superior, respectively. Used in DICOM.
    
    See Also:
    
    Constant Field Values
  - LPST
```
private static final int LPST
```
    Like LPS, but with time along the fourth axis.
    
    See Also:
    
    Constant Field Values
  - SCANNER_XYZ
```
private static final int SCANNER_XYZ
```
    A scanner-based right-handed coordinate frame, used in ACR/NEMA 2.0. If a patient lies parallel to the ground, face-up on the table, with their feet-to-head direction same as the front-to-back direction of the imaging equipment, the axes of this scanner-based coordinate frame and the (patient-based) left-posterior-superior frame coincide.
    
    See Also:
    
    Constant Field Values
  - SCANNER_XYZ_TIME
```
private static final int SCANNER_XYZ_TIME
```
    Like SCANNER_XYZ, but with time along the fourth axis.
    
    See Also:
    
    Constant Field Values
  - THREED_RIGHT_HANDED
```
private static final int THREED_RIGHT_HANDED
```
    Any right-handed three-dimensional space.
    
    See Also:
    
    Constant Field Values
  - THREED_LEFT_HANDED
```
private static final int THREED_LEFT_HANDED
```
    Any left-handed three-dimensional space.
    
    See Also:
    
    Constant Field Values
  - THREED_RIGHT_HANDED_TIME
```
private static final int THREED_RIGHT_HANDED_TIME
```
    Like THREED_RIGHT_HANDED, but with time along the fourth axis.
    
    See Also:
    
    Constant Field Values
  - THREED_LEFT_HANDED_TIME
```
private static final int THREED_LEFT_HANDED_TIME
```
    Like THREEE_LEFT_HANDED, but with time along the fourth axis.
    
    See Also:
    
    Constant Field Values
  - NONE
```
private static final int NONE
```
    Centering information for this axis is either meaningless or unknown. This applies to any non-spatial axis.
    
    See Also:
    
    Constant Field Values
  - CELL
```
private static final int CELL
```
    The location of the sample is located in the interior of the grid element.
    
    See Also:
    
    Constant Field Values
  - NODE
```
private static final int NODE
```
    The location of the sample is at the boundary between grid elements.
    
    See Also:
    
    Constant Field Values
  - apInvert
```
private boolean apInvert
```
    True for RAS and LAS, false for LPS. If true, change sign on origin[1] and row[1] of matrix.
  - autoSequence
```
private boolean autoSequence
```
    True if data file: [] encountered If true, autosequence using integer format specification varied according to , , and .
  - axisMaxs
```
private double[] axisMaxs
```
    Maximum axis value. centers[i], axisMins[i], axisMaxs[i], and nrrdSizes[i] are used to calculate resols[i] and origin[i] if spacings[i] not available.
  - axisMins
```
private double[] axisMins
```
    Minimum axis value. centers[i], axisMins[i], axisMaxs[i], and nrrdSizes[i] are used to calculate resols[i] and origin[i] if spacings[i] not available.
  - axisOrientation
```
private int[] axisOrientation
```
    For each axis R2L, L2R, A2P, P2A, I2S, or S2I
  - baseAfterNumber
```
private java.lang.String baseAfterNumber
```
    In autosequencing number between a capital D and the last period used in generating filenames. The capital D must come after the percentage sign.
  - baseBeforeNumber
```
private java.lang.String baseBeforeNumber
```
    In autosequencing number before percentage sign and period used in generating start of autosequenced filename.
  - baseNumber
```
private boolean baseNumber
```
    Used if autosequencing. If true, increment file base. If false, increment file extension. True if period follows a capital D. The capital D must follow a percentage sign.
  - centers
```
private int[] centers
```
    May remain null or may be created as NONE, CELL, or NODE.
  - dwmriGradient
```
private java.lang.String[][] dwmriGradient
```
    "modality:=DWMRI" : This key/value pair explicitly indicates that the image is a diffusion-weighted MRI scan, and it implies that all of the following key/value pairs are also set in the header: "DWMRI_b-value:=b " : This key/value pair gives the (scalar) diffusion-weighting value, in units of s/mm^2. Example: "DWMRI_b-value:=1000". The effective magnitude of diffusion-weighting for each DWI is determined with some simple calculations based on the individual per-DWI gradient directions or B-matrices. For every index position NNNN along the DWI axis (whichever is the non-spatial axis identified by the "list" or "vector" kind field), either "DWMRI_gradient_NNNN:=x y z " or "DWMRI_B-matrix_NNNN:=xx xy xz yy yz zz " must be given (except if "DWMRI_NEX_NNNN:= M " is used).
  - dwmriNex
```
private java.lang.String[][] dwmriNex
```
    "DWMRI_NEX_NNNN:=M " means that the information provided for image NNNN (either gradient or B-matrix) is the same as for image NNNN+1, NNNN+2, up to and including NNNN+M-1.
  - endianess
```
private boolean endianess
```
    DOCUMENT ME!
  - ext
```
private java.lang.String ext
```
    DOCUMENT ME!
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoNRRD fileInfo
```
    DOCUMENT ME!
  - fileInfoSub
```
private FileInfoNRRD fileInfoSub
```
    DOCUMENT ME!
  - fileLength
```
private long fileLength
```
    DOCUMENT ME!
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - fileNameSequence
```
private boolean fileNameSequence
```
    DOCUMENT ME!
  - fileNameSet
```
private java.lang.String[] fileNameSet
```
    DOCUMENT ME!
  - fileNumber
```
private int fileNumber
```
    DOCUMENT ME!
  - finishBlank
```
private int[] finishBlank
```
    DOCUMENT ME!
  - finishQuote
```
private int[] finishQuote
```
    DOCUMENT ME!
  - foundEOF
```
private boolean foundEOF
```
    DOCUMENT ME!
  - foundEOHeader
```
private boolean foundEOHeader
```
    DOCUMENT ME!
  - gunzip
```
private boolean gunzip
```
    If true, data has gzip compression.
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - imgExtents
```
private int[] imgExtents
```
    DOCUMENT ME!
  - kindsString
```
private java.lang.String[] kindsString
```
    Kind of information represented by the samples along each axis.
  - matrix
```
private TransMatrix matrix
```
    DOCUMENT ME!
  - measurementFrame
```
private double[][] measurementFrame
```
    The measurement frame is a basic (per-array) field specification (not per-axis), which identifies a spaceDim-by-spaceDim matrix, where spaceDim is the dimension of the word space (implied by space or given by space dimension). The matrix transforms (a column vector of) coordinates in the measurement frame to corrdinates in world space. vector[i] gives column i of the measurement frame matrix. Just as the space directions field gives, one column at a time, the mapping from image space to world space coordinates, the measurement frame gives the mapping measurement frame to world space coordinates, also one column at a time.
  - mipavDataType
```
private int mipavDataType
```
    DOCUMENT ME!
  - mipavDimensions
```
private int mipavDimensions
```
    DOCUMENT ME!
  - mipavLabels
```
private java.lang.String[] mipavLabels
```
    MIPAV axis names such as X, Y, or Z
  - mipavUnits
```
private int[] mipavUnits
```
    DOCUMENT ME!
  - nrrdDataType
```
private int nrrdDataType
```
    Does not tell if color or black and white.
  - nrrdDimensions
```
private int nrrdDimensions
```
    May not be the same as MIPAV dimensions because in nrrd color is a dimension.
  - nrrdLabels
```
private java.lang.String[] nrrdLabels
```
    nrrd axis names such as X, Y, or Z
  - nrrdSizes
```
private int[] nrrdSizes
```
    The number of samples along each nrrd axis
  - nrrdSpaceUnits
```
private java.lang.String[] nrrdSpaceUnits
```
    DOCUMENT ME!
  - nrrdUnits
```
private java.lang.String[] nrrdUnits
```
    Units of measurement of nrrd axis
  - numColors
```
private int numColors
```
    DOCUMENT ME!
  - numSpaceKinds
```
private int numSpaceKinds
```
    Number of nrrd dimensions for which the kinds string equals "SPACE".
  - numThicknesses
```
private int numThicknesses
```
    Number of axes for which thicknesses values found
  - offset1
```
private long offset1
```
    DOCUMENT ME!
  - oneFileStorage
```
private boolean oneFileStorage
```
    True for .nrrd file with header and data in the same file. False for .nhdr header files with the data in one or more other files.
  - origin
```
private float[] origin
```
    DOCUMENT ME!
  - paddingNumber
```
private int paddingNumber
```
    In autosequencing if the sequence number length is less than the padding number, zeroes are added to the front of the sequence number until the sequence number length equals the padding number.
  - planarConfig
```
private int planarConfig
```
    0 indicates pixels are RGB, RGB chunky 1 indicates pixels are RRR, GGG, BBB planar.
  - reorder
```
private boolean reorder
```
    The orientation information in some NRRD files cannot be applied to MIPAV without dimension reordering. This applies to 2 of my 15 example NRRD files. In Dwi-D.nhdr 4 dimensions are specified with the dimensions from 0 to 3 having sizes of 13, 29, 30, and 31. Right-anterior-superior space is specified, but the first axis contains diffusion values and the last 3 axes are the x, y, and z coordinates, so the right-anterior-space applies to the last 3 dimensions, whereas MIPAV would expect the first 3 dimensions to be involved. In gk2-rcc-mask2.nhdr 4 dimensions are specified with the dimensions from 0 to 3 having sizes of 7, 148, 190, and 160. Left-posterior-space is specified, but the first axis contains diffusion values and the last 3 axes are x, y, and z coordinates, so again the space applies to the last 3 dimensions rather than MIPAV's first 3 dimensions. In these cases reorder the data so that the first axis becomes the last axis.
  - resols
```
private float[] resols
```
    DOCUMENT ME!
  - RGBAOrder
```
private boolean RGBAOrder
```
    If true, data is a specialized form of 4-color with red, green, blue, and alpha, in that order.
  - rlInvert
```
private boolean rlInvert
```
    True for RAS. False for LAS and LPS. If true, change sign on origin[0] and first row of matrix.
  - sequenceFinish
```
private int sequenceFinish
```
    DOCUMENT ME!
  - sequenceStart
```
private int sequenceStart
```
    DOCUMENT ME!
  - sequenceStep
```
private int sequenceStep
```
    DOCUMENT ME!
  - skippedBytes
```
private int skippedBytes
```
    Number of bytes to skip
  - skippedLines
```
private int skippedLines
```
    Number of lines to skip
  - sliceThickness
```
private float sliceThickness
```
    DOCUMENT ME!
  - space
```
private int space
```
    RAS, LAS, LPS, RAST, LAST, LPST, SCANNER_XYZ, SCANNER_XYZ_TIME, THREED_RIGHT_HANDED, THREED_LEFT_HANDED, THREED_RIGHT_HANDED_TIME, or THREED_LEFT_HANDED_TIME
  - spaceDirections
```
private double[][] spaceDirections
```
    Second index of spaceDirections specifies row of matrix to set.
  - spaceOrigin
```
private double[] spaceOrigin
```
    Used to set origin values.
  - spaceUnitsString
```
private java.lang.String spaceUnitsString
```
    DOCUMENT ME!
  - spacings
```
private double[] spacings
```
    Resolutions values for nrrd axes
  - startBlank
```
private int[] startBlank
```
    DOCUMENT ME!
  - startQuote
```
private int[] startQuote
```
    DOCUMENT ME!
  - subdim
```
private int subdim
```
    DOCUMENT ME!
  - thicknesses
```
private double[] thicknesses
```
    Used to obtain MIPAV sliceThickness value
  - versionNumber
```
private float versionNumber
```
    Version of the NRRD file format being used.
  - oneFile
```
private boolean oneFile
```
    If true, header and data both stored in .nrrd file. If false, header stored in filename.nhdr and data stored in filename.raw.
  - writeVersionNumber
```
private static final int writeVersionNumber
```
    version number of NRRD for writing
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - FileNRRD
```
public FileNRRD(java.lang.String fName,
                java.lang.String fDir)
```
    Constructs new file object.
    
    Parameters:
    
    fName - File name.
    
    fDir - File directory.
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
    
    Overrides:
    
    finalize in class FileBase
  - getFileInfo
```
public FileInfoNRRD getFileInfo()
```
    Returns the FileInfoNRRD read from the file.
    
    Returns:
    
    File info read from file, or null if it has not been read.
  - readHeader
```
public boolean readHeader(java.lang.String imageFileName,
                          java.lang.String fileDir)
                   throws java.io.IOException
```
    Reads the NRRD header and stores the information in fileInfo.
    
    Parameters:
    
    imageFileName - File name of image.
    
    fileDir - Directory.
    
    Returns:
    
    Flag to confirm a successful read.
    
    Throws:
    
    java.io.IOException - if there is an error reading the header
    
    See Also:
    
    FileInfoNRRD
  - readImage
```
public ModelImage readImage(boolean one,
                            boolean doHeader)
                     throws java.io.IOException,
                            java.lang.OutOfMemoryError
```
    Reads a NRRD image file by reading the header then making a FileRaw to read the image for all filenames in the file list. Only the one file directory (currently) supported.
    
    Parameters:
    
    one - flag indicating one image of a 3D dataset should be read in.
    
    doHeader -
    
    Returns:
    
    The image.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
    
    java.lang.OutOfMemoryError
    
    See Also:
    
    FileRaw
  - getAxisOrientation
```
private int[] getAxisOrientation(TransMatrix mat)
```
    Return the 3 axis orientation codes that correspond to the closest standard anatomical orientation of the (i,j,k) axes.
    
    Parameters:
    
    mat - 4x4 matrix that transforms (i,j,k) indexes to x,y,z coordinates where +x =Left, +y = Posterior, +z = Superior Only the upper-left 3x3 corner of the matrix is used This routine finds the permutation of (x,y,z) which has the smallest angle to the (i,j,k) axes directions, which are columns of the input matrix Errors: The codes returned will be zero.
    
    Returns:
    
    codes
  - getOffset
```
private int getOffset(FileInfoNRRD fileInfo)
```
    Helper method to calculate the offset for getting only the middle NRRD image slice from the 3D file.
    
    Parameters:
    
    fileInfo - File info.
    
    Returns:
    
    offset
  - readLine
```
private java.lang.String readLine()
                           throws java.io.IOException
```
    Reads lines of the file and strips comments indicated by the # symbol until a nonnull String results or the end of the file is reached or a blank line containing end of header with zero characters is reached.
    
    Returns:
    
    the line read in
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - setFileInfo
```
public void setFileInfo(FileInfoNRRD fileInfo)
```
    Parameters:
    
    fileInfo -
  - setFileInfo
```
private void setFileInfo(FileInfoNRRD fileInfo,
                         ModelImage image)
```
    DOCUMENT ME!
    
    Parameters:
    
    fileInfo - -- a NRRD file Info that has already been read
    
    image - -- a ModelImage that the fileInfo needs to be attached to
  - updateorigins
```
private void updateorigins(FileInfoBase[] fileInfo)
```
    Updates the start locations. Each image has a fileinfo where the start locations are stored. Note that the start location for the Z (3rd) dimension change with the change is the slice. The origin is in the upper left corner and we are using the right hand rule. + x -> left to right; + y -> top to bottom and + z -> into screen.
    
    Parameters:
    
    fileInfo - DOCUMENT ME!
  - writeHeader
```
private boolean writeHeader(ModelImage image,
                            java.lang.String fhName,
                            java.lang.String fDir,
                            int beginSlice,
                            int endSlice,
                            int beginTime,
                            int endTime)
                     throws java.io.IOException
```
    write NRRD header
    
    Returns:
    
    Throws:
    
    java.io.IOException
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes a NRRD format type image.
    
    Parameters:
    
    image - Image model of data to write.
    
    options - FileWriteOptions
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeHeader3DTo2D
```
private void writeHeader3DTo2D(ModelImage img,
                               java.lang.String headerName,
                               java.lang.String headerDir,
                               FileWriteOptions options)
                        throws java.io.IOException
```
    Method to save off the header from a 3D image into 2D header files sequentially named (similar to the method in FileRaw).
    
    Parameters:
    
    img - Image to be saved
    
    headerName - Name of file
    
    headerDir - Directory for file
    
    options - File write options (contains # of digits and start #)
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - writeHeader4DTo3D
```
private void writeHeader4DTo3D(ModelImage image,
                               java.lang.String fileName,
                               java.lang.String fileDir,
                               FileWriteOptions options)
                        throws java.io.IOException
```
    This method is used when saving a 4D image in an array of 3D files. The file name has numbers appended to correctly order the images.
    
    Parameters:
    
    image - the image dataset to be saved
    
    fileName - the file name
    
    fileDir - the file directory
    
    options - file options indicate how to save the image
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!

Class FileNRRD

Field Summary

Fields inherited from class gov.nih.mipav.model.file.FileBase

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.file.FileBase

Methods inherited from class java.lang.Object

Field Detail

UNKNOWN

LPS

LPST

SCANNER_XYZ

SCANNER_XYZ_TIME

THREED_RIGHT_HANDED

THREED_LEFT_HANDED

THREED_RIGHT_HANDED_TIME

THREED_LEFT_HANDED_TIME

NONE

CELL

NODE

apInvert

autoSequence

axisMaxs

axisMins

axisOrientation

baseAfterNumber

baseBeforeNumber

baseNumber

centers

dwmriGradient

dwmriNex

endianess

ext

file

fileDir

fileInfo

fileInfoSub

fileLength

fileName

fileNameSequence

fileNameSet

fileNumber

finishBlank

finishQuote

foundEOF

foundEOHeader

gunzip

image

imgExtents

kindsString

matrix

measurementFrame

mipavDataType

mipavDimensions

mipavLabels

mipavUnits

nrrdDataType

nrrdDimensions

nrrdLabels

nrrdSizes

nrrdSpaceUnits

nrrdUnits

numColors

numSpaceKinds

numThicknesses

offset1

oneFileStorage

origin

paddingNumber

planarConfig

reorder

resols

RGBAOrder

rlInvert

sequenceFinish

sequenceStart

sequenceStep

skippedBytes

skippedLines

sliceThickness