java.lang.Object
- gov.nih.mipav.model.structures.ModelSerialCloneable
- - gov.nih.mipav.model.file.FileInfoBase
  - - gov.nih.mipav.model.file.FileInfoMincHDF

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable
```
public class FileInfoMincHDF
extends FileInfoBase
```
See Also:

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
`protected static int[]`	`axisOrientation`	The axis orientation static types
`private java.util.Hashtable<java.lang.String,java.lang.String>`	`dicomTable`	Hashtable to hold the tags for conversion to->from dicom and to-> mipav XML format
`private javax.swing.tree.DefaultMutableTreeNode`	`dimensionNode`	The dimension tree node that holds xspace, yspace, and (optionally) zspace nodes
`private boolean`	`hasImageMinMaxDimOrder`
`private javax.swing.tree.DefaultMutableTreeNode`	`imageNode`	The image node that holds information about the image data (rescaling, dimorder, actual data).
`private javax.swing.tree.DefaultMutableTreeNode`	`informationNode`	The information node that holds acquisition information, dicom tags, and more
`private static long`	`serialVersionUID`
`private double[]`	`validRange`	The valid range for image pixel values

Fields inherited from class gov.nih.mipav.model.file.FileInfoBase
ANGSTROMS, ANGSTROMS_STRING, AXIAL, 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

FileInfoMincHDF(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
`static void`	`calculateRescaleIntercept(double[] rescaleIntercept, double[] rescaleSlope, double[] imageMax, double[] imageMin, double[] valid_range, boolean hasImageMinMaxDimOrder)`	In MINC images, "real" values for pixels are calculated by taking the given image min and image max and rescaling the data accordingly.
`void`	`convertPatientInfo(FileInfoImageXML dInfo)`	Strips out the relevant patient info (if present) to insert into MIPAV's XML header
`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`	`displayAboutInfo(JDialogBase dlog, TransMatrix matrix)`	Displays important information about the image.
`double[]`	`getConvertStartLocationsToDICOM(double[] step, double[][] cosines, boolean[] isCentered, int slice, double[] mincStartLoc)`	Converts from the minc start location to the dicom start locations
`java.util.Hashtable<java.lang.String,java.lang.String>`	`getDicomTable()`	Retrieves the dicom converted tag hashtable
`javax.swing.tree.DefaultMutableTreeNode`	`getDimensionNode()`	Returns the dimension node (only 1 exists at fileinfo[0] position
`javax.swing.tree.DefaultMutableTreeNode`	`getImageNode()`	Returns the image node (image info and data)
`javax.swing.tree.DefaultMutableTreeNode`	`getInfoNode()`	Returns the information node with dicom/patient info
`double[]`	`getValidRange()`	Gets the valid range for image data values
`boolean`	`isHasImageMinMaxDimOrder()`
`void`	`setDicomTable(java.util.Hashtable<java.lang.String,java.lang.String> dTable)`	Sets the dicom converted tag hashtable
`void`	`setDimensionNode(javax.swing.tree.DefaultMutableTreeNode dimNode)`	Sets the dimension node (xspace, yspace and optional zspace nodes)
`void`	`setHasImageMinMaxDimOrder(boolean hasImageMinMaxDimOrder)`
`void`	`setImageNode(javax.swing.tree.DefaultMutableTreeNode imageNode)`	Sets the image node (includes image info and data)
`void`	`setInfoNode(javax.swing.tree.DefaultMutableTreeNode infoNode)`	Sets the information node (includes dicom tags and patient info
`void`	`setModality(java.lang.String modality)`	Sets the image modality based on the string
`void`	`setStartLocations(double[] origin)`	Sets start locations of each axis.
`void`	`setValidRange(double[] valid_range)`	Sets the valid range for the image data

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
```
    See Also:
    
    Constant Field Values
  - dimensionNode
```
private transient javax.swing.tree.DefaultMutableTreeNode dimensionNode
```
    The dimension tree node that holds xspace, yspace, and (optionally) zspace nodes
  - informationNode
```
private transient javax.swing.tree.DefaultMutableTreeNode informationNode
```
    The information node that holds acquisition information, dicom tags, and more
  - imageNode
```
private transient javax.swing.tree.DefaultMutableTreeNode imageNode
```
    The image node that holds information about the image data (rescaling, dimorder, actual data).
  - axisOrientation
```
protected static int[] axisOrientation
```
    The axis orientation static types
  - validRange
```
private double[] validRange
```
    The valid range for image pixel values
  - hasImageMinMaxDimOrder
```
private boolean hasImageMinMaxDimOrder
```
  - dicomTable
```
private transient java.util.Hashtable<java.lang.String,java.lang.String> dicomTable
```
    Hashtable to hold the tags for conversion to->from dicom and to-> mipav XML format
- Constructor Detail
  - FileInfoMincHDF
```
public FileInfoMincHDF(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
  - 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
  - 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
  - setDimensionNode
```
public void setDimensionNode(javax.swing.tree.DefaultMutableTreeNode dimNode)
```
    Sets the dimension node (xspace, yspace and optional zspace nodes)
    
    Parameters:
    
    dimNode - the dimension node
  - getDimensionNode
```
public javax.swing.tree.DefaultMutableTreeNode getDimensionNode()
```
    Returns the dimension node (only 1 exists at fileinfo[0] position
    
    Returns:
    
    the dimension node
  - setInfoNode
```
public void setInfoNode(javax.swing.tree.DefaultMutableTreeNode infoNode)
```
    Sets the information node (includes dicom tags and patient info
    
    Parameters:
    
    infoNode - the information node
  - getInfoNode
```
public javax.swing.tree.DefaultMutableTreeNode getInfoNode()
```
    Returns the information node with dicom/patient info
    
    Returns:
    
    the information node
  - setImageNode
```
public void setImageNode(javax.swing.tree.DefaultMutableTreeNode imageNode)
```
    Sets the image node (includes image info and data)
    
    Parameters:
    
    imageNode - the image node
  - isHasImageMinMaxDimOrder
```
public boolean isHasImageMinMaxDimOrder()
```
  - setHasImageMinMaxDimOrder
```
public void setHasImageMinMaxDimOrder(boolean hasImageMinMaxDimOrder)
```
  - getImageNode
```
public javax.swing.tree.DefaultMutableTreeNode getImageNode()
```
    Returns the image node (image info and data)
    
    Returns:
    
    the image node
  - setModality
```
public void setModality(java.lang.String modality)
```
    Sets the image modality based on the string
  - setValidRange
```
public void setValidRange(double[] valid_range)
```
    Sets the valid range for the image data
    
    Parameters:
    
    valid_range - double valid range of image data values
  - getValidRange
```
public double[] getValidRange()
```
    Gets the valid range for image data values
    
    Returns:
    
    the valid range (min to max) array
  - setDicomTable
```
public void setDicomTable(java.util.Hashtable<java.lang.String,java.lang.String> dTable)
```
    Sets the dicom converted tag hashtable
    
    Parameters:
    
    dTable - hashtable holding dicom keys and tags
  - getDicomTable
```
public java.util.Hashtable<java.lang.String,java.lang.String> getDicomTable()
```
    Retrieves the dicom converted tag hashtable
    
    Returns:
    
    the dicom hashtable
  - convertPatientInfo
```
public void convertPatientInfo(FileInfoImageXML dInfo)
```
    Strips out the relevant patient info (if present) to insert into MIPAV's XML header
    
    Parameters:
    
    dInfo - destination XML fileinfo
  - getConvertStartLocationsToDICOM
```
public final double[] getConvertStartLocationsToDICOM(double[] step,
                                                      double[][] cosines,
                                                      boolean[] isCentered,
                                                      int slice,
                                                      double[] mincStartLoc)
```
    Converts from the minc start location to the dicom start locations
    
    Parameters:
    
    step - the resolutions (step, can be negative)
    
    cosines - the directional matrix
    
    isCentered - is the axis centered
    
    slice - the slice number
    
    mincStartLoc - the original minc start location [x,y, opt z]
    
    Returns:
  - setStartLocations
```
public final void setStartLocations(double[] origin)
```
    Sets start locations of each axis.
    
    Parameters:
    
    origin - the image origin
  - calculateRescaleIntercept
```
public static void calculateRescaleIntercept(double[] rescaleIntercept,
                                             double[] rescaleSlope,
                                             double[] imageMax,
                                             double[] imageMin,
                                             double[] valid_range,
                                             boolean hasImageMinMaxDimOrder)
```
    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 -
    
    rescaleSlope -
    
    imageMax -
    
    imageMin -
    
    validMax -
    
    validMin -

Class FileInfoMincHDF

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

dimensionNode

informationNode

imageNode

axisOrientation

validRange

hasImageMinMaxDimOrder

dicomTable

Constructor Detail

FileInfoMincHDF

Method Detail

convertTagsToTable

displayAboutInfo

setDimensionNode

getDimensionNode

setInfoNode

getInfoNode

setImageNode

isHasImageMinMaxDimOrder

setHasImageMinMaxDimOrder

getImageNode

setModality

setValidRange

getValidRange

setDicomTable

getDicomTable

convertPatientInfo

getConvertStartLocationsToDICOM

setStartLocations

calculateRescaleIntercept