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

All Methods Static Methods Instance Methods Concrete Methods
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.

Class FileInfoMinc

Nested Class Summary

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

Field Summary

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

NC_BYTE

NC_CHAR

NC_SHORT

NC_INT

NC_FLOAT

NC_DOUBLE

NC_DIMENSION

NC_VARIABLE

NC_ATTRIBUTE

dicomToMincVarMap

numrecs

vmax

vmin

dimArray

gattArray

varArray

Constructor Detail

FileInfoMinc

Method Detail

addAttValue

addDimElem

addGattElem

addVarElem

anonymize

calculateIntercept

calculateRescaleIntercept

calculateSlope

convertTagsToTable

createDimArray

createGattArray

createVarArray

displayAboutInfo

getConvertStartLocationsToDICOM

getDicomValue

getDimArray

getDimElem

getGattArray

getGattElem

getStartLocations

getVarArray

getVarElem

setImportantImageInfo

setModality

setResolutions

setStartLocations

setUnits

getTagElem

getTagGroup

getAxisOrientation

getMincSliceThickness

setOrientType

setStartLocation