Package gov.nih.mipav.model.file

Class FileInfoMincHDF

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

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 -