Package gov.nih.mipav.model.file

Class FileInfoMinc

java.lang.Object

gov.nih.mipav.model.structures.ModelSerialCloneable

gov.nih.mipav.model.file.FileInfoBase

gov.nih.mipav.model.file.FileInfoMinc

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class FileInfoMinc
extends FileInfoBase

This class holds all the file information for a MINC file. In addition, it has three classes to organize the data.

MINC headers have three main parts: the dimensions, the global attributes, and the variables. There are typically three dimensions, representing the x, y, and z dimensions of the image. There is usually one global attribute, the history. There can be any number of variables.

Variables have within them any number of attributes. So for example, "rootvariable", the first variable in all the MINC files I have seen so far, has the following attributes: varid (= "MINC standard variable"), vartype (= "group________"), version (= "MINC version 1.0"), parent (blank), and children (image). Usually there is a variable for each dimension, a variable for the image, a variable for image min, and a variable for image max. There can also be variables containing patient information or anything else useful.

See the documentation for the classes MincDimElem, MincAttElem, and MincVarElem for further information. The classes are structured exactly like a MINC file.

Version:

1.0 July 1, 2000

See Also:

FileMinc, Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.model.file.FileInfoBase

FileInfoBase.AxisOrientation, FileInfoBase.ImageOrientation, FileInfoBase.Modality, FileInfoBase.Unit, FileInfoBase.UnitType

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String[]	dicomToMincVarMap	Minc var equivalents to anonymizable Dicom tags.
private FileMincDimElem[]	dimArray	DOCUMENT ME!
private FileMincAttElem[]	gattArray	DOCUMENT ME!
static int	NC_ATTRIBUTE	NetCDF defined data type - attribute.
static int	NC_BYTE	NetCDF defined data type - byte.
static int	NC_CHAR	NetCDF defined data type - character.
static int	NC_DIMENSION	NetCDF defined data type - dimension.
static int	NC_DOUBLE	NetCDF defined data type - double.
static int	NC_FLOAT	NetCDF defined data type - float.
static int	NC_INT	NetCDF defined data type - integer.
static int	NC_SHORT	NetCDF defined data type - short.
static int	NC_VARIABLE	NetCDF defined data type - variable.
int	numrecs	DOCUMENT ME!
private static long	serialVersionUID	Use serialVersionUID for interoperability.
private FileMincVarElem[]	varArray	DOCUMENT ME!
double	vmax	Valid image maximum value.
double	vmin	Valid image minimum value.

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

ANGSTROMS, ANGSTROMS_STRING, AXIAL, axisOrientation, axisOrientationStr, BIOMAGNETIC_IMAGING, cameraMake, cameraModel, CENTIMETERS, CENTIMETERS_STRING, COLOR_FLOW_DOPPLER, COMPRESSION_BZIP2, COMPRESSION_GZIP, COMPRESSION_NONE, COMPRESSION_ZIP, COMPUTED_RADIOGRAPHY, COMPUTED_TOMOGRAPHY, conversionSpaceTimeUnits, CORONAL, DEGREES, DEGREES_STRING, DIAPHANOGRAPHY, DIGITAL_RADIOGRAPHY, DUPLEX_DOPPLER, ENDOSCOPY, exposureTime, EXTERNAL_CAMERA_PHOTOGRAPHY, FA, fileName, fileSuffix, FNumber, focalLength, focalLength35, GENERAL_MICROSCOPY, HARDCOPY, HOURS, HOURS_STRING, HZ, HZ_STRING, ICG, imageOrientation, INCHES, INCHES_STRING, INTRAORAL_RADIOGRAPHY, ISOSpeedRating, KILOMETERS, KILOMETERS_STRING, LASER_SURFACE_SCAN, MAGNETIC_RESONANCE, MAGNETIC_RESONANCE_ANGIOGRAPHY, MAGNETIC_RESONANCE_SPECTROSCOPY, MAMMOGRAPHY, METERS, METERS_STRING, MICROMETERS, MICROMETERS_STRING, MICROSEC, MICROSEC_STRING, MILES, MILES_STRING, MILLIMETERS, MILLIMETERS_STRING, MILLISEC, MILLISEC_STRING, MILS, MILS_STRING, MINUTES, MINUTES_STRING, modality, NANOMETERS, NANOMETERS_STRING, NANOSEC, NANOSEC_STRING, NUCLEAR_MEDICINE, ORI_A2P_TYPE, ORI_I2S_TYPE, ORI_L2R_TYPE, ORI_P2A_TYPE, ORI_R2L_TYPE, ORI_S2I_TYPE, ORI_UNKNOWN_TYPE, origin, OTHER, PANORAMIC_XRAY, POSITRON_EMISSION_TOMOGRAPHY, PPM, PPM_STRING, RADIO_FLUOROSCOPY, RADIOGRAPHIC_IMAGING, RADIOTHERAPY_DOSE, RADIOTHERAPY_IMAGE, RADIOTHERAPY_PLAN, RADIOTHERAPY_RECORD, RADIOTHERAPY_STRUCTURE_SET, RADS, RADS_STRING, RED_FREE, SAGITTAL, SECONDS, SECONDS_STRING, SINGLE_PHOTON_EMISSION_COMPUTED_TOMOGRAPHY, SLIDE_MICROSCOPY, sUnits, tagDescription, tagName, THERMOGRAPHY, TRANSFORM_ANOTHER_DATASET, TRANSFORM_MNI_152, TRANSFORM_SCANNER_ANATOMICAL, TRANSFORM_TALAIRACH_TOURNOUX, TRANSFORM_UNKNOWN, tUnits, ULTRASOUND, unitsOfMeasure, UNKNOWN_MEASURE, UNKNOWN_MODALITY, UNKNOWN_ORIENT, UNKNOWN_STRING, XRAY_ANGIOGRAPHY

Constructor Summary

Constructors

Constructor	Description
FileInfoMinc(java.lang.String name, java.lang.String directory, int format)	MINC file information constructor.

Method Summary

Modifier and Type	Method	Description
void	addAttValue(FileMincAttElem elem, java.lang.Object value, int index)	Sets the value of the attribute element; used for setting attribute of variables.
void	addDimElem(java.lang.String name, int length, int index)	Puts a new dimension element with the specified parameters into the dimension array at the gievn index.
void	addGattElem(java.lang.String name, int type, int length, int index)	Puts a new global attribute array element with the specified parameters into the global attribute array at the given index.
void	addVarElem(java.lang.String name, int nelems, int[] dimid, int index)	Puts a new variable element with the specified paramenters into the array at the given index.
void	anonymize(boolean[] list)	Removes requested identifying info.
static double	calculateIntercept(double min, double slope, double validMin)	Calculates rescale intercept given a min and a slope value.
void	calculateRescaleIntercept(double[] rescaleIntercept, double[] rescaleSlope)	In MINC images, "real" values for pixels are calculated by taking the given image min and image max and rescaling the data accordingly.
static double	calculateSlope(double max, double min, double validMax, double validMin)	Calculates rescale slope given a min and a max value.
java.util.Hashtable<java.lang.String,java.lang.String>	convertTagsToTable()	Returns all of the dicom-converted tags in the minc header as a tag-value hashtable.
void	createDimArray(int length)	Constructs the dimension array with the specified length.
void	createGattArray(int length)	Constructs the global attribute array with the specified length.
void	createVarArray(int length)	Constructs the variable array with the specified length.
void	displayAboutInfo(JDialogBase dlog, TransMatrix matrix)	Displays important information about the image.
static int[]	getAxisOrientation(TransMatrix mat)	Return the 3 axis orientation codes that correspond to the closest standard anatomical orientation of the (i,j,k) axes.
double[]	getConvertStartLocationsToDICOM(int slice, int time)	Accessor that gets the "start" variable values, adjusted so that [0] holds the image x axis value, [1] the image y axis value, and [2] the image z axis value.
java.lang.String	getDicomValue(java.lang.String dicomTag)	Get the value from the minc info based on a given dicom tag id.
FileMincDimElem[]	getDimArray()	Gets the array with the dimension information.
FileMincDimElem	getDimElem(int index)	Accessor that returns the dimension element at the indicated index in the dimension array.
FileMincAttElem[]	getGattArray()	Gets the array with the attribute information.
FileMincAttElem	getGattElem(int index)	Accessor that returns the global attribute element at the indicated index in the global attribute array.
private double	getMincSliceThickness()	Return the slice thickness value stored in the minc header (var = 'acquisition', attrib = 'slice_thickness').
float[]	getStartLocations()	Accessor that gets the "start" variable values, with the "xspace" in 0, "yspace" in 1, and "zspace" in 2.
private static java.lang.String	getTagElem(java.lang.String fullTag)	Extract the element identifier (removing the group id).
private static java.lang.String	getTagGroup(java.lang.String fullTag)	Extract the group to which a dicom or minc element belongs to.
FileMincVarElem[]	getVarArray()	Gets the array with the variable information.
FileMincVarElem	getVarElem(int index)	Accessor that returns the variable element at the indicated index in the variable array.
void	setImportantImageInfo()	Sets necessary image information.
void	setModality()	Sets the image modality based on the.
static int	setOrientType(java.lang.String space, boolean positive)	Helper method to set the axis orientations.
void	setResolutions(int orientation)	Sets the resolutions from the variable array based on the orientation of the image.
private void	setStartLocation(double originCoord, int axis)	Sets the start location of the specified axis.
void	setStartLocations(double[] origin)	Sets start locations of each axis.
void	setUnits()	Sets the units of the dimensions, as in millimeters, inches, etc.

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

copyCoreInfo, copyCoreInfo, displayAboutInfo, displayPrimaryInfo, finalize, getAboutInfo, getAllSameDimUnits, getAreaUnitsOfMeasureStr, getAxisDirection, getAxisOrientation, getAxisOrientation, getAxisOrientationFromStr, getAxisOrientationStr, getCameraMake, getCameraModel, getCompressionType, getDataType, getDataTypeFromStr, getEndianess, getEndianessFromStr, getExposureTime, getExtents, getFileDirectory, getFileFormat, getFileName, getFileSuffix, getFNumber, getFocalLength, getFocalLength35, getImageOrientation, getImageOrientationFromStr, getImageOrientationStr, getIs2_5D, getISOSpeedRating, getLPSOrigin, getLUT, getMax, getMaxB, getMaxG, getMaxR, getMin, getMinB, getMinG, getMinR, getModality, getModalityFromStr, getModalityStr, getModalityStr, getMultiFile, getNumOfBytesPerPixel, getOffset, getOrigin, getOrigin, getOriginalEndianess, getOriginAtSlice, getPhotometric, getPixelPadValue, getPrimaryInfo, getRescaleIntercept, getRescaleSlope, getResolution, getResolutions, getSize, getSliceThickness, getUnitsOfMeasure, getUnitsOfMeasure, getUnitsOfMeasureAbbrevStr, getUnitsOfMeasureAbbrevStr, getUnitsOfMeasureFromStr, getUnitsOfMeasureStr, getUnitsOfMeasureStr, getVolumeUnitsOfMeasureStr, isDicomOrdered, oppositeOrient, sameAxis, setAxisOrientation, setAxisOrientation, setCameraMake, setCameraModel, setCompressionType, setDataType, setEndianess, setExposureTime, setExtents, setExtents, setFileDirectory, setFileFormat, setFileName, setFileSuffix, setFNumber, setFocalLength, setFocalLength35, setImageOrientation, setISOSpeedRating, setLUT, setMax, setMaxB, setMaxG, setMaxR, setMin, setMinB, setMinG, setMinR, setModality, setMultiFile, setOffset, setOrigin, setOrigin, setOriginalEndianess, setPhotometric, setPixelPadValue, setRescaleIntercept, setRescaleSlope, setResolutions, setResolutions, setSliceThickness, setTagDescription, setTagName, setUnitsOfMeasure, setUnitsOfMeasure, setUnitsOfMeasure, setUnitsOfMeasure, toString

Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneable

clone, nativeClone

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

serialVersionUID

private static final long serialVersionUID

Use serialVersionUID for interoperability.

See Also:

Constant Field Values

NC_BYTE

public static final int NC_BYTE

NetCDF defined data type - byte.

See Also:

Constant Field Values

NC_CHAR

public static final int NC_CHAR

NetCDF defined data type - character.

See Also:

Constant Field Values

NC_SHORT

public static final int NC_SHORT

NetCDF defined data type - short.

See Also:

Constant Field Values

NC_INT

public static final int NC_INT

NetCDF defined data type - integer.

See Also:

Constant Field Values

NC_FLOAT

public static final int NC_FLOAT

NetCDF defined data type - float.

See Also:

Constant Field Values

NC_DOUBLE

public static final int NC_DOUBLE

NetCDF defined data type - double.

See Also:

Constant Field Values

NC_DIMENSION

public static final int NC_DIMENSION

NetCDF defined data type - dimension.

See Also:

Constant Field Values

NC_VARIABLE

public static final int NC_VARIABLE

NetCDF defined data type - variable.

See Also:

Constant Field Values

NC_ATTRIBUTE

public static final int NC_ATTRIBUTE

NetCDF defined data type - attribute.

See Also:

Constant Field Values

dicomToMincVarMap

public static final java.lang.String[] dicomToMincVarMap

Minc var equivalents to anonymizable Dicom tags. Must be in the same order as FileInfoDicom.anonymizeTagIDs.

See Also:

FileInfoDicom.anonymizeTagIDs

numrecs

public int numrecs

DOCUMENT ME!

vmax

public double vmax

Valid image maximum value. Default = -1.

vmin

public double vmin

Valid image minimum value. Default = -1.

dimArray

private FileMincDimElem[] dimArray

DOCUMENT ME!

gattArray

private FileMincAttElem[] gattArray

DOCUMENT ME!

varArray

private FileMincVarElem[] varArray

DOCUMENT ME!

Constructor Detail

FileInfoMinc

public FileInfoMinc(java.lang.String name,
                    java.lang.String directory,
                    int format)

MINC file information constructor.

Parameters:

name - file name

directory - file directory

format - format (in this case, MINC)

Method Detail

addAttValue

public void addAttValue(FileMincAttElem elem,
                        java.lang.Object value,
                        int index)

Sets the value of the attribute element; used for setting attribute of variables. A MincVarElem has an array of attributes and this method is called on those attributes.

Parameters:

elem - the attribute element to add the value to.

value - the value to set the element to.

index - the index into the value array to set this value at.

See Also:

FileMincAttElem.setValue(java.lang.Object, int)

addDimElem

public void addDimElem(java.lang.String name,
                       int length,
                       int index)

Puts a new dimension element with the specified parameters into the dimension array at the gievn index. The name is usually xspace, yspace, or zspace; the length is the corresponding size of that dimension.

Parameters:

name - the name of the dimension element

length - the length of the dimension element

index - the index to put this element into the array

addGattElem

public void addGattElem(java.lang.String name,
                        int type,
                        int length,
                        int index)

Puts a new global attribute array element with the specified parameters into the global attribute array at the given index. Usually there is only one element in the global attribute array: the history.

Parameters:

name - the name of the global attribute element

type - the data type, i.e. byte, char, int, etc (see statically defined types)

length - the length of the element

index - the index into the array to put this element at

addVarElem

public void addVarElem(java.lang.String name,
                       int nelems,
                       int[] dimid,
                       int index)

Puts a new variable element with the specified paramenters into the array at the given index. There are other attributes to set for variables, in particular the attribute array, but that gets set in a different place.

Parameters:

name - the name of this variable element

nelems - the number of elements in the attribute array

dimid - the dimension id array, usually empty but for "image" containing information about the dimensions

index - index into the variable array to put this variable

See Also:

FileMincVarElem

anonymize

public final void anonymize(boolean[] list)

Removes requested identifying info. Can remove info stored in the minc header in a dicom-like structure and in a more minc-like info structure.

Parameters:

list - the list of tags to remove; it MUST correspond to anonymizeTagIDs list (or spurious errors result), and it must be of the same length, or this will throw an IllegalArgumentException.

Throws:

java.lang.IllegalArgumentException - DOCUMENT ME!

calculateIntercept

public static final double calculateIntercept(double min,
                                              double slope,
                                              double validMin)

Calculates rescale intercept given a min and a slope value.

Parameters:

min - Min value.

slope - Slope value.

Returns:

Rescale intercept.

calculateRescaleIntercept

public void calculateRescaleIntercept(double[] rescaleIntercept,
                                      double[] rescaleSlope)

In MINC images, "real" values for pixels are calculated by taking the given image min and image max and rescaling the data accordingly. Image min and image max are given per slice.

Parameters:

rescaleIntercept - Array of rescale intercepts to set

rescaleSlope - Array of rescale slopes to set

calculateSlope

public static final double calculateSlope(double max,
                                          double min,
                                          double validMax,
                                          double validMin)

Calculates rescale slope given a min and a max value.

Parameters:

max - Max value.

min - Min value.

Returns:

Rescale slope

convertTagsToTable

public java.util.Hashtable<java.lang.String,java.lang.String> convertTagsToTable()

Returns all of the dicom-converted tags in the minc header as a tag-value hashtable.

Returns:

a tag-value hashtable

createDimArray

public final void createDimArray(int length)

Constructs the dimension array with the specified length.

Parameters:

length - the length of the array

createGattArray

public final void createGattArray(int length)

Constructs the global attribute array with the specified length.

Parameters:

length - the length of the array

createVarArray

public final void createVarArray(int length)

Constructs the variable array with the specified length.

Parameters:

length - the length of the array

displayAboutInfo

public void displayAboutInfo(JDialogBase dlog,
                             TransMatrix matrix)

Displays important information about the image.

Specified by:

displayAboutInfo in class FileInfoBase

Parameters:

dlog - where to display the info

matrix - the transformation matrix

getConvertStartLocationsToDICOM

public final double[] getConvertStartLocationsToDICOM(int slice,
                                                      int time)

Accessor that gets the "start" variable values, adjusted so that [0] holds the image x axis value, [1] the image y axis value, and [2] the image z axis value.

MINC positive axis is left to right; positive axis is posterior to anterior; postive axis is inferior to superior

DICOM positive axis is right to left; positive axis is anterior to posterior; postive axis is inferior to superior

If the space's alignment attribute has the value 'centre', then subtract half the space's step value (doesn't seem to apply to zspace for some reason..). Then transform the point by the inverse of the direction_cosines matrix (extracted from the spaces). The result then has some of the signs of its components flipped (which is determined by the image orientation) to get it from minc to dicom orientation.

Parameters:

slice - slice to begin the start variable on.

timeSlice - time to begin the start variable on

Returns:

The slice position in dicom (and mipav) space.

getDicomValue

public java.lang.String getDicomValue(java.lang.String dicomTag)

Get the value from the minc info based on a given dicom tag id.

Parameters:

dicomTag - dicom tag (group,elem)

Returns:

the value stored in the info (or null if it doesn't exist)

getDimArray

public final FileMincDimElem[] getDimArray()

Gets the array with the dimension information.

Returns:

the array

getDimElem

public final FileMincDimElem getDimElem(int index)

Accessor that returns the dimension element at the indicated index in the dimension array.

Parameters:

index - index where the dimension element is located

Returns:

dimArray[index]

getGattArray

public final FileMincAttElem[] getGattArray()

Gets the array with the attribute information.

Returns:

the array

getGattElem

public final FileMincAttElem getGattElem(int index)

Accessor that returns the global attribute element at the indicated index in the global attribute array.

Parameters:

index - index where the global attribute element is located

Returns:

gattArray[index]

getStartLocations

public final float[] getStartLocations()

Accessor that gets the "start" variable values, with the "xspace" in 0, "yspace" in 1, and "zspace" in 2. This differs from the other methods because it doesn't place the values so that they correspond to image x, y, and z. Gets values as stored in MINC header, not modified to account for the different origin.

Returns:

The "start" values for the image.

getVarArray

public final FileMincVarElem[] getVarArray()

Gets the array with the variable information.

Returns:

the array

getVarElem

public final FileMincVarElem getVarElem(int index)

Accessor that returns the variable element at the indicated index in the variable array.

Parameters:

index - index where the variable element is located

Returns:

varArray[index]

setImportantImageInfo

public final void setImportantImageInfo()

Sets necessary image information.

setModality

public void setModality()

Sets the image modality based on the.

setResolutions

public void setResolutions(int orientation)

Sets the resolutions from the variable array based on the orientation of the image. The "zspace" in MINC refers to the inferior-superior axis, whereas in MIPAV the z resolution variable is the slices (space between slices) regardless of the orientation. Therefore for proper display we must convert between them.

Parameters:

orientation - The orientation of the image (sagittal, coronal, or axial).

setStartLocations

public final void setStartLocations(double[] origin)

Sets start locations of each axis.

Parameters:

origin - the image origin

setUnits

public final void setUnits()

Sets the units of the dimensions, as in millimeters, inches, etc. Called after the header has been read in so the values within the varArray have been set properly already.

getTagElem

private static java.lang.String getTagElem(java.lang.String fullTag)

Extract the element identifier (removing the group id).

Parameters:

fullTag - the full element identitfier

Returns:

the element id

getTagGroup

private static java.lang.String getTagGroup(java.lang.String fullTag)

Extract the group to which a dicom or minc element belongs to.

Parameters:

fullTag - the full element identitfier

Returns:

the element group

getAxisOrientation

public static 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 = Right, +y = Anterior, +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

getMincSliceThickness

private double getMincSliceThickness()

Return the slice thickness value stored in the minc header (var = 'acquisition', attrib = 'slice_thickness').

Returns:

The slice thickness, if it is stored in the minc header (0 otherwise).

setOrientType

public static int setOrientType(java.lang.String space,
                                boolean positive)

Helper method to set the axis orientations.

Parameters:

space - The space - "xspace", "yspace", or "zspace".

positive - Flag indicating if the space is moving in a positive direction.

Returns:

The proper axis orientation for that space.

setStartLocation

private void setStartLocation(double originCoord,
                              int axis)

Sets the start location of the specified axis.

Parameters:

originCoord - origin coord.

axis - Axis of orientation; x is 0, y is 1, z is 2.