Class FileInfoBase

    • Field Detail

      • serialVersionUID

        private static final long serialVersionUID
        Use serialVersionUID for interoperability.
        See Also:
        Constant Field Values
      • sUnits

        public static final java.lang.String[] sUnits
        Deprecated.
        Array of space units: inches, mm, etc.
      • tUnits

        public static final java.lang.String[] tUnits
        Deprecated.
        Array of time units: seconds, minutes, etc.
      • UNKNOWN_MEASURE

        public static final int UNKNOWN_MEASURE
        Unit of measurement unknown.
        See Also:
        Constant Field Values
      • MILS

        public static final int MILS
        Units of measurement mil (thousandth of an inch)
        See Also:
        Constant Field Values
      • CENTIMETERS

        public static final int CENTIMETERS
        Unit of measurement centimeters.
        See Also:
        Constant Field Values
      • ANGSTROMS

        public static final int ANGSTROMS
        Unit of measurement angstroms.
        See Also:
        Constant Field Values
      • NANOMETERS

        public static final int NANOMETERS
        Unit of measurement nanometers.
        See Also:
        Constant Field Values
      • MICROMETERS

        public static final int MICROMETERS
        Unit of measurement micrometers.
        See Also:
        Constant Field Values
      • MILLIMETERS

        public static final int MILLIMETERS
        Unit of measurement millimeters.
        See Also:
        Constant Field Values
      • KILOMETERS

        public static final int KILOMETERS
        Unit of measurement kilometers.
        See Also:
        Constant Field Values
      • NANOSEC

        public static final int NANOSEC
        Unit of measurement nanoseconds.
        See Also:
        Constant Field Values
      • MICROSEC

        public static final int MICROSEC
        Unit of measurement microseconds.
        See Also:
        Constant Field Values
      • MILLISEC

        public static final int MILLISEC
        Unit of measurement milliseconds.
        See Also:
        Constant Field Values
      • UNKNOWN_STRING

        public static final java.lang.String UNKNOWN_STRING
        String version of units of measurement - unknown.
        See Also:
        Constant Field Values
      • INCHES_STRING

        public static final java.lang.String INCHES_STRING
        String version of units of measurement - inches.
        See Also:
        Constant Field Values
      • MILS_STRING

        public static final java.lang.String MILS_STRING
        String version of units of measurement - mils.
        See Also:
        Constant Field Values
      • CENTIMETERS_STRING

        public static final java.lang.String CENTIMETERS_STRING
        String version of units of measurement - centimeters.
        See Also:
        Constant Field Values
      • ANGSTROMS_STRING

        public static final java.lang.String ANGSTROMS_STRING
        String version of units of measurement - angstroms.
        See Also:
        Constant Field Values
      • NANOMETERS_STRING

        public static final java.lang.String NANOMETERS_STRING
        String version of units of measurement - nanometers.
        See Also:
        Constant Field Values
      • MICROMETERS_STRING

        public static final java.lang.String MICROMETERS_STRING
        String version of units of measurement - micrometers.
        See Also:
        Constant Field Values
      • MILLIMETERS_STRING

        public static final java.lang.String MILLIMETERS_STRING
        String version of units of measurement - millimeters.
        See Also:
        Constant Field Values
      • METERS_STRING

        public static final java.lang.String METERS_STRING
        String version of units of measurement - meters.
        See Also:
        Constant Field Values
      • KILOMETERS_STRING

        public static final java.lang.String KILOMETERS_STRING
        String version of units of measurement - kilometers.
        See Also:
        Constant Field Values
      • MILES_STRING

        public static final java.lang.String MILES_STRING
        String version of units of measurement - miles.
        See Also:
        Constant Field Values
      • NANOSEC_STRING

        public static final java.lang.String NANOSEC_STRING
        String version of units of measurement - nanoseconds.
        See Also:
        Constant Field Values
      • MICROSEC_STRING

        public static final java.lang.String MICROSEC_STRING
        String version of units of measurement - microseconds.
        See Also:
        Constant Field Values
      • MILLISEC_STRING

        public static final java.lang.String MILLISEC_STRING
        String version of units of measurement - milliseconds.
        See Also:
        Constant Field Values
      • SECONDS_STRING

        public static final java.lang.String SECONDS_STRING
        String version of units of measurement - seconds.
        See Also:
        Constant Field Values
      • MINUTES_STRING

        public static final java.lang.String MINUTES_STRING
        String version of units of measurement - minutes.
        See Also:
        Constant Field Values
      • HOURS_STRING

        public static final java.lang.String HOURS_STRING
        String version of units of measurement - hours.
        See Also:
        Constant Field Values
      • HZ_STRING

        public static final java.lang.String HZ_STRING
        String version of units of measurement - hertz.
        See Also:
        Constant Field Values
      • PPM_STRING

        public static final java.lang.String PPM_STRING
        String version of units of measurement - part-per-million.
        See Also:
        Constant Field Values
      • RADS_STRING

        public static final java.lang.String RADS_STRING
        String version of units of measurement - radians per second.
        See Also:
        Constant Field Values
      • DEGREES_STRING

        public static final java.lang.String DEGREES_STRING
        String version of units of measurement - degrees.
        See Also:
        Constant Field Values
      • conversionSpaceTimeUnits

        public static final double[] conversionSpaceTimeUnits
        Deprecated.
        should use enum conversions
        Converting between space units. Conversion is to millimeters (the default). Table converts to mm by multiplication. Converts from mm by division. Example: inches * 25.4f = mm mm / 25.4f = inches. Converting between time units. Conversion is to seconds(the default). Table converts to seconds by multiplication. Converts from seconds by division. Example: minutes * 0.01667 = seconds seconds / 0.01667 = minutes. Hertz and radians per second convert to/from hz. parts-per-million does not convert.
      • UNKNOWN_MODALITY

        public static final int UNKNOWN_MODALITY
        Image modality unknown.
        See Also:
        Constant Field Values
      • BIOMAGNETIC_IMAGING

        public static final int BIOMAGNETIC_IMAGING
        Image modality biomagnetic imaging.
        See Also:
        Constant Field Values
      • COLOR_FLOW_DOPPLER

        public static final int COLOR_FLOW_DOPPLER
        Image modality color flow doppler.
        See Also:
        Constant Field Values
      • COMPUTED_RADIOGRAPHY

        public static final int COMPUTED_RADIOGRAPHY
        Image modality CR.
        See Also:
        Constant Field Values
      • COMPUTED_TOMOGRAPHY

        public static final int COMPUTED_TOMOGRAPHY
        Image modality CT.
        See Also:
        Constant Field Values
      • DUPLEX_DOPPLER

        public static final int DUPLEX_DOPPLER
        Image modality duplex doppler.
        See Also:
        Constant Field Values
      • DIAPHANOGRAPHY

        public static final int DIAPHANOGRAPHY
        Image modality diaphanography.
        See Also:
        Constant Field Values
      • DIGITAL_RADIOGRAPHY

        public static final int DIGITAL_RADIOGRAPHY
        Image modality digital radiography.
        See Also:
        Constant Field Values
      • GENERAL_MICROSCOPY

        public static final int GENERAL_MICROSCOPY
        Image modality general microscopy.
        See Also:
        Constant Field Values
      • INTRAORAL_RADIOGRAPHY

        public static final int INTRAORAL_RADIOGRAPHY
        Image modality intraoral radiography.
        See Also:
        Constant Field Values
      • LASER_SURFACE_SCAN

        public static final int LASER_SURFACE_SCAN
        Image modality laser surface scan.
        See Also:
        Constant Field Values
      • MAGNETIC_RESONANCE_ANGIOGRAPHY

        public static final int MAGNETIC_RESONANCE_ANGIOGRAPHY
        Image modality MR angiography.
        See Also:
        Constant Field Values
      • MAMMOGRAPHY

        public static final int MAMMOGRAPHY
        Image modality mammography.
        See Also:
        Constant Field Values
      • MAGNETIC_RESONANCE

        public static final int MAGNETIC_RESONANCE
        Image modality MR.
        See Also:
        Constant Field Values
      • MAGNETIC_RESONANCE_SPECTROSCOPY

        public static final int MAGNETIC_RESONANCE_SPECTROSCOPY
        Image modality MR SPECT.
        See Also:
        Constant Field Values
      • NUCLEAR_MEDICINE

        public static final int NUCLEAR_MEDICINE
        Image modality nuclear medicine.
        See Also:
        Constant Field Values
      • POSITRON_EMISSION_TOMOGRAPHY

        public static final int POSITRON_EMISSION_TOMOGRAPHY
        Image modality PET.
        See Also:
        Constant Field Values
      • PANORAMIC_XRAY

        public static final int PANORAMIC_XRAY
        Image modality panoramtic X ray.
        See Also:
        Constant Field Values
      • RADIO_FLUOROSCOPY

        public static final int RADIO_FLUOROSCOPY
        Image modality radio fluoroscopy.
        See Also:
        Constant Field Values
      • RADIOGRAPHIC_IMAGING

        public static final int RADIOGRAPHIC_IMAGING
        Image modality radiographic imaging.
        See Also:
        Constant Field Values
      • RADIOTHERAPY_DOSE

        public static final int RADIOTHERAPY_DOSE
        Image modality radiotherapy dose.
        See Also:
        Constant Field Values
      • RADIOTHERAPY_IMAGE

        public static final int RADIOTHERAPY_IMAGE
        Image modality radiotherapy image.
        See Also:
        Constant Field Values
      • RADIOTHERAPY_PLAN

        public static final int RADIOTHERAPY_PLAN
        Image modality radiotherapy plan.
        See Also:
        Constant Field Values
      • RADIOTHERAPY_RECORD

        public static final int RADIOTHERAPY_RECORD
        Image modality radiotherapy record.
        See Also:
        Constant Field Values
      • RADIOTHERAPY_STRUCTURE_SET

        public static final int RADIOTHERAPY_STRUCTURE_SET
        Image modality radiotherapy structure set.
        See Also:
        Constant Field Values
      • SLIDE_MICROSCOPY

        public static final int SLIDE_MICROSCOPY
        Image modality slide microscopy.
        See Also:
        Constant Field Values
      • SINGLE_PHOTON_EMISSION_COMPUTED_TOMOGRAPHY

        public static final int SINGLE_PHOTON_EMISSION_COMPUTED_TOMOGRAPHY
        Image modality SPECT.
        See Also:
        Constant Field Values
      • THERMOGRAPHY

        public static final int THERMOGRAPHY
        Image modality thermography.
        See Also:
        Constant Field Values
      • ULTRASOUND

        public static final int ULTRASOUND
        Image modality ultrasound.
        See Also:
        Constant Field Values
      • XRAY_ANGIOGRAPHY

        public static final int XRAY_ANGIOGRAPHY
        Image modality X ray angiography.
        See Also:
        Constant Field Values
      • EXTERNAL_CAMERA_PHOTOGRAPHY

        public static final int EXTERNAL_CAMERA_PHOTOGRAPHY
        Image modality external camera photography.
        See Also:
        Constant Field Values
      • modalityStr

        private static final java.lang.String[] modalityStr
        Deprecated.
        No longer needed since enum works now
        Array of modality strings -- again, numbering starts at 1, not 0.
      • ORI_UNKNOWN_TYPE

        public static final int ORI_UNKNOWN_TYPE
        Axis orientation unknown.
        See Also:
        Constant Field Values
      • ORI_R2L_TYPE

        public static final int ORI_R2L_TYPE
        Axis orientation Right to Left.
        See Also:
        Constant Field Values
      • ORI_L2R_TYPE

        public static final int ORI_L2R_TYPE
        Axis orientation Left to Right.
        See Also:
        Constant Field Values
      • ORI_P2A_TYPE

        public static final int ORI_P2A_TYPE
        Axis orientation Posterior to Anterior.
        See Also:
        Constant Field Values
      • ORI_A2P_TYPE

        public static final int ORI_A2P_TYPE
        Axis orientation Anterior to Posterior.
        See Also:
        Constant Field Values
      • ORI_I2S_TYPE

        public static final int ORI_I2S_TYPE
        Axis orientation Inferior to Superior.
        See Also:
        Constant Field Values
      • ORI_S2I_TYPE

        public static final int ORI_S2I_TYPE
        Axis orientation Superior to Inferior.
        See Also:
        Constant Field Values
      • axisOrientationStr

        public static final java.lang.String[] axisOrientationStr
        Array of axis orientation strings.
      • UNKNOWN_ORIENT

        public static final int UNKNOWN_ORIENT
        Unknown orientation.
        See Also:
        Constant Field Values
      • imageOrientationStr

        private static final java.lang.String[] imageOrientationStr
        Array of image orientation strings.
      • TRANSFORM_UNKNOWN

        public static final int TRANSFORM_UNKNOWN
        Unknown transform ID.
        See Also:
        Constant Field Values
      • TRANSFORM_SCANNER_ANATOMICAL

        public static final int TRANSFORM_SCANNER_ANATOMICAL
        Scanner Anatomical transform ID.
        See Also:
        Constant Field Values
      • TRANSFORM_ANOTHER_DATASET

        public static final int TRANSFORM_ANOTHER_DATASET
        Another Dataset transform ID.
        See Also:
        Constant Field Values
      • TRANSFORM_TALAIRACH_TOURNOUX

        public static final int TRANSFORM_TALAIRACH_TOURNOUX
        Talairach Tournoux transform ID.
        See Also:
        Constant Field Values
      • TRANSFORM_MNI_152

        public static final int TRANSFORM_MNI_152
        MNI 152 transform ID.
        See Also:
        Constant Field Values
      • COMPRESSION_NONE

        public static final int COMPRESSION_NONE
        Indicates no compression.
        See Also:
        Constant Field Values
      • COMPRESSION_ZIP

        public static final int COMPRESSION_ZIP
        Indicates zip compression of an image.
        See Also:
        Constant Field Values
      • COMPRESSION_GZIP

        public static final int COMPRESSION_GZIP
        Indicates gzip compression of an image.
        See Also:
        Constant Field Values
      • COMPRESSION_BZIP2

        public static final int COMPRESSION_BZIP2
        Indicates bzip2 compression of an image.
        See Also:
        Constant Field Values
      • axisOrientation

        protected int[] axisOrientation
        axis orientation used to support image ordering and display for medical images. We support the right hand rule where the origin is the upper left hand of the image with the positive axis.

        x - left to right y - top to botton z - into the screen

      • fileName

        protected java.lang.String fileName
        The file name which includes the path information.
      • fileSuffix

        protected java.lang.String fileSuffix
        File suffix (ex. "jpg")
      • imageOrientation

        protected int imageOrientation
        Indicates the image orientation (i.e. Axial, Coronal, ...)
      • modality

        protected int modality
        Indicates the modality (medical image type) of the dataset.
      • origin

        protected float[] origin
        The origin to support image locations (ie. DICOM, MINC ...) it is relative to the image origin. the positive axis are right hand rule.

        x - left to right y - top to botton z - into the screen

      • compressionType

        private int compressionType
        Used to indicate if the raw data was also compression (0 = no, 1 = zip).
      • dataType

        private int dataType
        The data type of the data (i.e. byte, short, float ...
      • dimResolutions

        private float[] dimResolutions
        Pixel or voxel resolutions for each dimension - default = 1.0. The z-dim resolution should be the spacing between the centers of adjacent slices; sometimes this will match the slice thickness, but not always.
      • endianess

        private boolean endianess
        The Endianess of the data. Intel, DEC Alpha ***** LSB first byte LITTLE_ENDIAN (false) Motorola (MAC), SPARC (SUN), SGI IRIX MSB first byte BIG_ENDIAN (true)
      • originalEndianess

        private boolean originalEndianess
        Used for checking for endianess changes in the ModelImage.reallocate(final int type) function.
      • extents

        private int[] extents
        Image extents as decribed by the image file format.
      • fileFormat

        private int fileFormat
        File format as defined in the Filebase.
      • max

        private double max
        Image maximum intensity for single channel image.
      • maxB

        private double maxB
        Image maximum intensity for the blue channel of an RGB image.
      • maxG

        private double maxG
        Image maximum intensity for the green channel of an RGB image.
      • maxR

        private double maxR
        Image maximum intensity for the red channel of an RGB image.
      • min

        private double min
        Image minimum intensity for single channel image.
      • minB

        private double minB
        Image minimum intensity for the blue channel of an RGB image.
      • minG

        private double minG
        Image minimum intensity for the green channel of an RGB image.
      • minR

        private double minR
        Image minimum intensity for the red channel of an RGB image.
      • lut

        private ModelLUT lut
        ModelLUT associated with fileinfo
      • multiFile

        private boolean multiFile
        Flag that indicates whether or not the image is in multiple files (tiff).
      • offset

        private int offset
        Number of bytes to the start the image data - ie. the header length
      • photometric

        private short photometric
        Image minimum intensity for single channel image.
      • pixelPadValue

        private java.lang.Short pixelPadValue
        Some file formats have a pad value for pixels outside the acquisition domain.
      • rescaleIntercept

        private double rescaleIntercept
        DICOM images have a rescale y-intercept value that we have also kept in the base.
      • rescaleSlope

        private double rescaleSlope
        DICOM images have a rescale slope value that we have also kept in the base.
      • sliceThickness

        private float sliceThickness
        The thickness of individual slices in the image volume. Stored in dicom tag 0018,0050 and various other places in other file formats.
      • unitsOfMeasure

        protected FileInfoBase.Unit[] unitsOfMeasure
        Describes the units of measure for the dataset.
      • tagName

        protected java.util.Vector<java.lang.String> tagName
      • tagDescription

        protected java.util.Vector<java.lang.String> tagDescription
      • focalLength

        protected double focalLength
      • focalLength35

        protected double focalLength35
      • cameraMake

        protected java.lang.String cameraMake
      • cameraModel

        protected java.lang.String cameraModel
      • exposureTime

        protected double exposureTime
      • FNumber

        protected double FNumber
      • ISOSpeedRating

        protected double ISOSpeedRating
    • Constructor Detail

      • FileInfoBase

        public FileInfoBase​(java.lang.String name,
                            java.lang.String directory,
                            int format)
        fileInfo constructor.
        Parameters:
        name - name of file
        directory - file directory
        format - file storage format -- see FileBase.java
      • FileInfoBase

        protected FileInfoBase​(FileInfoBase copy)
        Internal constructor for clone usage.
    • Method Detail

      • displayAboutInfo

        public abstract void displayAboutInfo​(JDialogBase dialog,
                                              TransMatrix matrix)
        Abstract method which is used by the extending class to display information about the window.
        Parameters:
        dialog - Area where image information is to be displayed.
        matrix - Transformation matrix
      • getAboutInfo

        public java.lang.String getAboutInfo​(TransMatrix matrix)
        Abstract method which is used by the extending class to return information about the file header.
        Parameters:
        matrix - Transformation matrix
        Returns:
        A string containing information from the image header.
      • copyCoreInfo

        public static void copyCoreInfo​(FileInfoBase[] originalInfo,
                                        FileInfoBase[] newInfo)
        Helper method to copy important file info type to another file info type.
        Parameters:
        originalInfo - source file info.
        newInfo - destination file info.
      • copyCoreInfo

        public static void copyCoreInfo​(FileInfoBase[] originalInfo,
                                        FileInfoBase[] newInfo,
                                        boolean[] listNoCopy)
        Helper method to copy core information from one fileinfo into another, this method also has a list of fileinfos NOT to copy (used by JDialogRemoveSlices).
        Parameters:
        originalInfo - FileInfoBase[] original file infos (longer list)
        newInfo - FileInfoBase[] new file infos (shorter list)
        listNoCopy - boolean[] boolean array of indices into the original fileinfos that should not be copied
      • getAxisOrientationFromStr

        public static int getAxisOrientationFromStr​(java.lang.String s)
        Returns the axis orientation associated with a string.
        Parameters:
        s - String to test
        Returns:
        axis orientation
      • getAxisOrientationStr

        public static java.lang.String getAxisOrientationStr​(int m)
        Return the string associated with an axis orientation.
        Parameters:
        m - int representing the axis orientation (see the static definitions)
        Returns:
        String representing the string associated with the axis orientation.
      • getDataTypeFromStr

        public static int getDataTypeFromStr​(java.lang.String s)
        Returns the image data type associated with a string.
        Parameters:
        s - String to test
        Returns:
        data type
      • getEndianessFromStr

        public static boolean getEndianessFromStr​(java.lang.String s)
        Returns the endianess associated with a string.
        Parameters:
        s - String to test
        Returns:
        Big endian or little endian
      • getImageOrientationFromStr

        public static int getImageOrientationFromStr​(java.lang.String s)
        Returns the image orientation associated with a string.
        Parameters:
        s - String to test
        Returns:
        image orientation
      • getImageOrientationStr

        public static java.lang.String getImageOrientationStr​(int m)
        Return the string associated with an image orientation.
        Parameters:
        m - the orientation (see the static definitions)
        Returns:
        the string associated with the orientation.
      • getModalityFromStr

        public static int getModalityFromStr​(java.lang.String s)
        Returns the modality associated with a string.
        Parameters:
        s - String to test
        Returns:
        modality
      • getModalityStr

        public static java.lang.String[] getModalityStr()
        Return all the modality strings as an array.
        Returns:
        String[] - array containing the strings associated with modalities.
      • getModalityStr

        public static java.lang.String getModalityStr​(int m)
        Return the string associated with a modality.
        Parameters:
        m - the modality (see the static definitions)
        Returns:
        the string associated with the modality.
      • getNumOfBytesPerPixel

        public static int getNumOfBytesPerPixel​(int dataType)
        Returns the number of bytes per pixel based on the data type.
        Parameters:
        dataType - the data type.
        Returns:
        the number of bytes per pixel.
        Throws:
        java.lang.IllegalArgumentException - DOCUMENT ME!
      • oppositeOrient

        public static int oppositeOrient​(int orient)
        Helper method that returns the opposite axis orientation of the one sent in; that is, R2L for L2R, A2P for P2A, etc.
        Parameters:
        orient - DOCUMENT ME!
        Returns:
        int Opposite image orientation
      • sameAxis

        public static boolean sameAxis​(int axisA,
                                       int axisB)
        Helper method to determine if axis A and axis B are the same axis: that is, if both are the patient x-axis, they will be either R2L or L2R.
        Parameters:
        axisA - Axis A: one of the defined ORI_ types.
        axisB - Axis B: one of the defined ORI_ types.
        Returns:
        boolean true if axis A and axis B are the same axis
      • displayAboutInfo

        public void displayAboutInfo​(JDialogBase dialog)
        Displays the file information.
        Parameters:
        dialog - dialog box that is written to
      • displayPrimaryInfo

        public void displayPrimaryInfo​(JDialogText dialog,
                                       TransMatrix matrix)
        Method called by many extending classes to display basic information in the dialog common to all images.
        Parameters:
        dialog - Area where image information is to be displayed.
        matrix - Transformation matrix
      • getPrimaryInfo

        public java.lang.String getPrimaryInfo​(TransMatrix matrix)
        Method called by many extending classes to return basic information in the dialog common to all images.
        Parameters:
        matrix - Transformation matrix
        Returns:
        The basic image header infomation.
      • finalize

        public void finalize()
        Prepares this class for cleanup.
        Overrides:
        finalize in class java.lang.Object
      • getAxisDirection

        public int[] getAxisDirection()
        Get the direction for accessing each axis of data. This is based on the values in the axisOrientation array.
        Returns:
        int[] Array of +/-1 values with one entry for each axis. A -1 indicates that the direction is reversed.
      • getAxisOrientation

        public int[] getAxisOrientation()
        Returns orientation of each axis.
        Returns:
        int[] orientation of each axis
        See Also:
        setAxisOrientation(int[])
      • getAxisOrientation

        public int getAxisOrientation​(int axis)
        Returns orientation of entered axis.
        Parameters:
        axis - Axis to get orientation for
        Returns:
        int orientation of specified axis
        See Also:
        setAxisOrientation(int, int)
      • getCompressionType

        public int getCompressionType()
        Gets the compression type.
        Returns:
        the compression type
      • getDataType

        public final int getDataType()
        Returns data type.
        Returns:
        int type of data in file
      • getEndianess

        public final boolean getEndianess()
        Descibes file endianess.
        Returns:
        boolean false = litteEndian format true = bigEndian format
      • getOriginalEndianess

        public final boolean getOriginalEndianess()
      • getExtents

        public final int[] getExtents()
        Returns the dimensionality of the image.
        Returns:
        int[] units (Inches or millimeters);
      • getFileDirectory

        public final java.lang.String getFileDirectory()
        Returns counter to start of image data.
        Returns:
        String that indicates location of the file
      • getFileFormat

        public final int getFileFormat()
        Returns file format.
        Returns:
        int file format (TIFF, raw, Analyze...)
      • getFileName

        public final java.lang.String getFileName()
        Returns the file name.
        Returns:
        String indicating file name
      • getFileSuffix

        public final java.lang.String getFileSuffix()
        Returns the file suffix.
        Returns:
        String representing the filename suffix
      • getImageOrientation

        public final int getImageOrientation()
        Returns the image orientation.
        Returns:
        int representing orientation
      • getIs2_5D

        public final boolean getIs2_5D()
        Return whether or not the image's slices are time based.
        Returns:
        boolean is 2.5 D
      • getLPSOrigin

        public float[] getLPSOrigin()
        DOCUMENT ME!
        Returns:
        float[] LPSOrigin
      • getLUT

        public ModelLUT getLUT()
        Returns the LUT.
      • getMax

        public final double getMax()
        Returns max pixel value of the image.
        Returns:
        double Returns double max pixel value of the image
      • getMaxB

        public final double getMaxB()
        Returns max blue pixel value of the image.
        Returns:
        double Returns double blue max pixel value of the image
      • getMaxG

        public final double getMaxG()
        Returns max green pixel value of the image.
        Returns:
        double Returns double green max pixel value of the image
      • getMaxR

        public final double getMaxR()
        Returns max red pixel value of the image.
        Returns:
        double Returns double red max pixel value of the image
      • getMin

        public final double getMin()
        Returns min pixel value of the image.
        Returns:
        double Returns double min pixel value of the image
      • getMinB

        public final double getMinB()
        Returns min blue pixel value of the image.
        Returns:
        double Returns double blue min pixel value of the image
      • getMinG

        public final double getMinG()
        Returns min green pixel value of the image.
        Returns:
        couble Returns double green min pixel value of the image
      • getMinR

        public final double getMinR()
        Returns min red pixel value of the image.
        Returns:
        couble Returns double red min pixel value of the image
      • getModality

        public final int getModality()
        Returns the modality.
        Returns:
        int indicating modality
      • getMultiFile

        public final boolean getMultiFile()
        Returns whether or not the image is in multiple files (tiff).
        Returns:
        boolean true indicates multiple files, false o.w.
      • getOffset

        public final int getOffset()
        Returns the header offset.
        Returns:
        int header offset
      • getOrigin

        public float[] getOrigin()
        Returns the origin.
        Returns:
        float[] the origin
      • getOrigin

        public float getOrigin​(int axis)
        Returns the origin value of the requested axis.
        Parameters:
        axis - requested axis; x is 0, y is 1, z is 2
        Returns:
        float orientation of axis
      • getOriginAtSlice

        public float[] getOriginAtSlice​(int slice)
        Gets the origin of a particular slice; resets for the z dimension.
        Parameters:
        slice - Z-dimension slice.
        Returns:
        float[] New start locations
      • getPhotometric

        public final short getPhotometric()
        Photometric interpretion.
        1 indicates 0 is black
        0 indicates 0 is white
        2 RGB
        3 indexed color LUT is saved with image
        4 Transparency Mask
        Returns:
        short Returns interpretation
      • getPixelPadValue

        public final java.lang.Short getPixelPadValue()
        Returns pixel pad value.
        Returns:
        Short Returns pixel pad value
      • getRescaleIntercept

        public final double getRescaleIntercept()
        Returns the intercept.
        Returns:
        double rescale intercept
      • getRescaleSlope

        public final double getRescaleSlope()
        Returns the slope.
        Returns:
        double rescale slope
      • getResolution

        public final float getResolution​(int dim)
        Returns the resolution of the requested dimension.
        Parameters:
        dim - The dimension to return the resolution of.
        Returns:
        The resolution of one of the image dimensions.
      • getResolutions

        public final float[] getResolutions()
        Returns each dimension's resolution.
        Returns:
        float[] dimension resolutions
      • getSize

        public int getSize()
        Returns the size of the slice image in byte which represented by this object.
        Returns:
        the size of the slice image in byte which represented by this object.
      • getSliceThickness

        public final float getSliceThickness()
        Returns the thickness of the image slices.
        Returns:
        slice thickness
      • getUnitsOfMeasure

        public final int[] getUnitsOfMeasure()
        Returns the units of measure.
        Returns:
        int[] units (Inches or millimeters);
      • getUnitsOfMeasure

        public int getUnitsOfMeasure​(int dim)
        Returns the units of measure for the given dimension.
        Parameters:
        dim - dimension index
        Returns:
        int units (Inches or millimeters);
      • getVolumeUnitsOfMeasureStr

        public java.lang.String getVolumeUnitsOfMeasureStr()
        Returns the volume unit for the data. Assumes all three dimensions are the same units.
        Returns:
        String associated volume unit of measure.
      • getAreaUnitsOfMeasureStr

        public java.lang.String getAreaUnitsOfMeasureStr()
        Returns the area unit for the data. Assumes both dimensions are the same units.
        Returns:
        String associated volume unit of measure.
      • isDicomOrdered

        public boolean isDicomOrdered()
        isDicomOrdered() returns true if the file is in dicom order, false otherwise.
        Returns:
        true if the file is in dicom order, false otherwise
      • setAxisOrientation

        public void setAxisOrientation​(int[] axOrient)
        Sets (copies) orientation of each axis.
        Parameters:
        axOrient - axis orientation array
        See Also:
        getAxisOrientation()
      • setAxisOrientation

        public void setAxisOrientation​(int axOrient,
                                       int axis)
        Sets the image orientation in the specified axis. Creates the axisOrientation if the array has not yet been created.
        Parameters:
        axOrient - orientation
        axis - axis of orientation; x is 0, y is 1, z is 2.
      • setCompressionType

        public void setCompressionType​(int type)
        Sets the compression type.
        Parameters:
        type - compression type
      • setDataType

        public final void setDataType​(int type)
        Sets format of image data.
        Parameters:
        type - data type defined in ModelStorageBase
      • setEndianess

        public void setEndianess​(boolean endness)
        Describes file endianess.
        Parameters:
        endness - endianess of the file format
      • setOriginalEndianess

        public void setOriginalEndianess​(boolean originalEndness)
      • setExtents

        public final void setExtents​(int[] dims)
        Sets dimensionality of the images.
        Parameters:
        dims - dimensionality for x,y, and z ... dimensions
      • setExtents

        public void setExtents​(int extent,
                               int dim)
        Sets dimensionality for image, on a per dimension basis.
        Parameters:
        extent - Extent of this dimension
        dim - Dimension to set extent in
      • setFileDirectory

        public final void setFileDirectory​(java.lang.String directory)
        DOCUMENT ME!
        Parameters:
        directory - DOCUMENT ME!
      • setFileFormat

        public final void setFileFormat​(int format)
        Sets the file format.
        Parameters:
        format - File format
      • setFileName

        public void setFileName​(java.lang.String fname)
        Sets the file name.
        Parameters:
        fname - image file name
      • setFileSuffix

        public final void setFileSuffix​(java.lang.String suffix)
        Sets the file suffix.
        Parameters:
        suffix - file suffix
      • setImageOrientation

        public void setImageOrientation​(int orient)
        Sets the image orientation.
        Parameters:
        orient - Orientation.
      • setLUT

        public void setLUT​(ModelLUT lut)
        Sets the model lut
        Parameters:
        reference - to the model lut for this file info (often shared between file infos to conserve space
      • setMax

        public void setMax​(double Max)
        Sets max pixel value of image.
        Parameters:
        Max - max pixel value
      • setMaxB

        public final void setMaxB​(double Max)
        Sets max blue pixel value of image.
        Parameters:
        Max - max blue pixel value
      • setMaxG

        public void setMaxG​(double Max)
        Sets max green pixel value of image.
        Parameters:
        Max - max green pixel value
      • setMaxR

        public void setMaxR​(double Max)
        Sets max red pixel value of image.
        Parameters:
        Max - max red pixel value
      • setMin

        public final void setMin​(double Min)
        Sets min pixel value of image.
        Parameters:
        Min - Min pixel value
      • setMinB

        public final void setMinB​(double Min)
        Sets min blue pixel value of image.
        Parameters:
        Min - min blue pixel value
      • setMinG

        public final void setMinG​(double Min)
        Sets min green pixel value of image.
        Parameters:
        Min - min green pixel value
      • setMinR

        public final void setMinR​(double Min)
        Sets min red pixel value of image.
        Parameters:
        Min - min red pixel value
      • setModality

        public final void setModality​(int mod)
        Sets the modality.
        Parameters:
        mod - modality
      • setMultiFile

        public final void setMultiFile​(boolean flag)
        Sets the flag for multiple files.
        Parameters:
        flag - true indicates multiple files for image, false o.w.
      • setOffset

        public final void setOffset​(int off)
        Sets the header offset.
        Parameters:
        off - the header offset
      • setOrigin

        public void setOrigin​(float[] originlocat)
        Sets the origin.
        Parameters:
        originlocat - origin location array
        See Also:
        #getStartLocations()
      • setOrigin

        public void setOrigin​(float originCoord,
                              int axis)
        Sets the start location in the specified axis. creates the startLocations if the arrray has not yet been created.
        Parameters:
        originCoord - start location
        axis - axis of orientation; x is 0, y is 1, z is 2
        See Also:
        #getStartLocations(int)
      • setPhotometric

        public void setPhotometric​(short value)
        Sets photometric interpretation.
        1 indicates 0 is black
        0 indicates 0 is white
        2 RGB
        3 indexed color LUT is saved with image
        Parameters:
        value - photometric value
      • setPixelPadValue

        public final void setPixelPadValue​(java.lang.Short value)
        Sets pixel pad value: used in some Dicom images.
        Parameters:
        value - pixel pad value
      • setRescaleIntercept

        public final void setRescaleIntercept​(double intercept)
        Sets the rescale intercept.
        Parameters:
        intercept - the intercept
      • setRescaleSlope

        public final void setRescaleSlope​(double slope)
        Sets the rescale slope.
        Parameters:
        slope - the slope
      • setResolutions

        public final void setResolutions​(float[] resolutions)
        Sets the resolutions of the image.
        Parameters:
        resolutions - resolution object
      • setResolutions

        public final void setResolutions​(float resolution,
                                         int dim)
        Sets the resolutions of the image, on a per dimension basis.
        Parameters:
        resolution - Resolution for the dimension
        dim - Dimension to set resolution in
      • setSliceThickness

        public void setSliceThickness​(float thickness)
        Sets the thickness of the image slices.
        Parameters:
        thickness - The slice thickness.
      • setUnitsOfMeasure

        public final void setUnitsOfMeasure​(FileInfoBase.Unit[] unitMeasure)
        Sets (copies) units of measure for image.
        Parameters:
        unitMeasure - unit of measure for a specified dimension
      • setUnitsOfMeasure

        public final void setUnitsOfMeasure​(int[] unitMeasure)
        Sets (copies) units of measure for image.
        Parameters:
        unitMeasure - unit of measure for a specified dimension
      • setUnitsOfMeasure

        public final void setUnitsOfMeasure​(FileInfoBase.Unit unitMeasure,
                                            int dim)
        Sets units of measure for image, on a per dimension basis.
        Parameters:
        unitMeasure - Unit of measure for the dimension
        dim - Dimension to set unit of measure in
      • setUnitsOfMeasure

        public final void setUnitsOfMeasure​(int unitMeasure,
                                            int dim)
        Sets units of measure for image, on a per dimension basis.
        Parameters:
        unitMeasure - Unit of measure for the dimension
        dim - Dimension to set unit of measure in
      • setTagName

        public void setTagName​(java.util.Vector<java.lang.String> tagName)
      • setTagDescription

        public void setTagDescription​(java.util.Vector<java.lang.String> tagDescription)
      • setFocalLength

        public void setFocalLength​(double focalLength)
      • getFocalLength

        public double getFocalLength()
      • setFocalLength35

        public void setFocalLength35​(double focalLength35)
      • getFocalLength35

        public double getFocalLength35()
      • setCameraMake

        public void setCameraMake​(java.lang.String cameraMake)
      • getCameraMake

        public java.lang.String getCameraMake()
      • setCameraModel

        public void setCameraModel​(java.lang.String cameraModel)
      • getCameraModel

        public java.lang.String getCameraModel()
      • setExposureTime

        public void setExposureTime​(double exposureTime)
      • getExposureTime

        public double getExposureTime()
      • setFNumber

        public void setFNumber​(double FNumber)
      • getFNumber

        public double getFNumber()
      • setISOSpeedRating

        public void setISOSpeedRating​(double ISOSpeedRating)
      • getISOSpeedRating

        public double getISOSpeedRating()
      • toString

        public java.lang.String toString()
        Gives the information contained in FileInfo in a string.
        Overrides:
        toString in class java.lang.Object
        Returns:
        String information contained in the FileInfo object
      • getUnitsOfMeasureAbbrevStr

        public static java.lang.String getUnitsOfMeasureAbbrevStr​(int i)
        Deprecated.
        should now use enum
        Parameters:
        i -
        Returns:
      • getUnitsOfMeasureStr

        public static java.lang.String getUnitsOfMeasureStr​(int xUnits)
        Deprecated.
        should now use enum
        Parameters:
        xUnits -
        Returns:
      • getUnitsOfMeasureFromStr

        public static int getUnitsOfMeasureFromStr​(java.lang.String selectedOutput)
        Deprecated.
        should now use enum
        Parameters:
        selectedOutput -
        Returns:
      • getAllSameDimUnits

        public static int[] getAllSameDimUnits​(int measure)
        Deprecated.
        should now use enum
        Parameters:
        selectedOutput -
        Returns:
      • getUnitsOfMeasureAbbrevStr

        public static java.lang.String[] getUnitsOfMeasureAbbrevStr()
        Deprecated.
        should now use enum
        Return all the abbreviated units of measure strings as an array.
        Returns:
        String[] - array containing the abbreviated strings associated with units of measure.
      • getUnitsOfMeasureStr

        public static java.lang.String[] getUnitsOfMeasureStr()
        Deprecated.
        should use enum
        Return all the units of measure strings as an array.
        Returns:
        String[] - array containing the strings associated with units of measure.