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

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable
```
public class FileInfoAnalyze
extends FileInfoBase
```
This structures contains the information that describes how an analyze image is stored on disk. Analyze Version 7.5. We have extended this format to store image orientation and origin. We have used unused variables to store these data. Almost all programs ignore these variables and should not have any problems reading images saved with MIPAV, except SPM. A new format for MIPAV is now XML based.
Unused1 - X-axis orientation @see FileInfoBase for static variables that are set. Unused2 - Y-axis orientation // All three unused variables are of short type. Unused3 - Z-axis orientation

Funused1 - X-axis starting location (origin from upper left-hand corner) Funused2 - Y-axis starting location (origin from upper left-hand corner) Funused3 - Z-axis starting location (origin is the first image slice)

RGB analyze images are store in chunky format rgb, rgb, rgb ......

Note that there is a char data_type[10] field and a short datatype field.

Version:

1.0 July, 2002

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

FileAnalyze, 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
`private java.lang.String`	`aux_file`	DOCUMENT ME!
`private short`	`bitpix`	Bits per pixel.
`private float`	`cal_max`	Range of calibration values.
`private float`	`cal_min`	Values of 0.0 for both fields imply that no calibration min and max values are used !
`private java.lang.String`	`cal_units`	Specifies the name of the calibration unit.
`private float`	`compressed`	Indicates if compression is used.
`static byte`	`CORONAL_FLIPPED`	DOCUMENT ME!
`static byte`	`CORONAL_UNFLIPPED`	DOCUMENT ME!
`private java.lang.String`	`data_type`	Unknown use 10 chars.
`private short`	`datatype`	Stores the image data type DT_NONE = 0; DT_UNKNOWN = 0; DT_BINARY = 1; DT_UNSIGNED_CHAR = 2; DT_SIGNED_SHORT = 4; DT_UNSIGNED_SHORT = 4; DT_SIGNED_INT = 8; DT_FLOAT = 16; DT_COMPLEX = 32; DT_DOUBLE = 64; DT_RGB = 128; DT_ALL = 255;
`private java.lang.String`	`db_name`	Name of file with a length of 18 chars.
`private java.lang.String`	`descrip`	String with a max character length of 80 used to describe image.
`private short`	`dim_un0`	Unused.
`static short`	`DT_ALL`	Analyze file format define use to indicate _ALL_ image data type.
`static short`	`DT_BINARY`	Analyze file format define use to indicate binary (1 bit) image data type.
`static short`	`DT_COMPLEX`	Analyze file format define use to indicate complex (64 bit) image data type.
`static short`	`DT_DOUBLE`	Analyze file format define use to indicate double (64 bit) image data type.
`static short`	`DT_FLOAT`	Analyze file format define use to indicate float (32 bit) image data type.
`static short`	`DT_NONE`	Analyze file format define use to indicate no image data type.
`static short`	`DT_RGB`	Analyze file format define use to indicate color (RGB - 24 bits) image data type.
`static short`	`DT_SIGNED_INT`	Analyze file format define use to indicate integer (32 bit) image data type.
`static short`	`DT_SIGNED_SHORT`	Analyze file format define use to indicate short (16 bit) image data type.
`static short`	`DT_UNKNOWN`	AAnalyze file format define use to indicate undefined image data type.
`static short`	`DT_UNSIGNED_CHAR`	Analyze file format define use to indicate unsigned byte (char) (8 bit) image data type.
`static short`	`DT_UNSIGNED_SHORT`	Analyze file format define use to indicate short (16 bit) image data type.
`private java.lang.String`	`exp_date`	String with a max character length of 10 used to indicate the experiment date.
`private java.lang.String`	`exp_time`	String with a max character length of 10 used to indicate the experiment time.
`private int`	`extents`	Should be 16384.
`private int`	`field_skip`	Unknown length.
`private float`	`funused1`	MIPAV uses this variable to define the X-axis origin.
`private float`	`funused2`	MIPAV uses this variable to define the Y-axis origin.
`private float`	`funused3`	MIPAV uses this variable to define the Z-axis origin.
`private java.lang.String`	`generated`	Unknown use.
`private int`	`glmax`	Maximum pixel values for the entire dataset.
`private int`	`glmin`	Minimum pixel values for the entire database.
`private java.lang.String`	`hist_un0`	Unknown use.
`private char`	`hkey_un0`	Unknown use.
`private int`	`omax`	Unknown use.
`private int`	`omin`	Unknown use.
`private byte`	`orient`	DOCUMENT ME!
`private java.lang.String`	`originator`	Unknown use.
`private java.lang.String`	`patient_id`	Patient's ID.
`private char`	`regular`	I think it means data has uniform spacing (resolutions).
`static byte`	`SAGITTAL_FLIPPED`	DOCUMENT ME!
`static byte`	`SAGITTAL_UNFLIPPED`	DOCUMENT ME!
`private java.lang.String`	`scannum`	Scan ID Length of 10.
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private short`	`session_error`	Unknown use.
`private int`	`sizeof_hdr`	Always of length 348.
`private int`	`smax`	Unknown use.
`private int`	`smin`	Unknown use.
`private int`	`start_field`	Unknown use.
`static byte`	`TRANSVERSE_FLIPPED`	DOCUMENT ME!
`static byte`	`TRANSVERSE_UNFLIPPED`	DOCUMENT ME!
`static byte`	`UNKNOWN_ORIENT`	The data_history substructure is not required, but the orient element is used to indicate individual slice orientation and determines whetther the Analyze Movie program will attempt to flip the images before displaying a movie sequence. 0 - transverse unflipped 1 - coronal unflipped 2 - sagitttal unflipped 3 - transverse flipped 4 - coronal flipped 5 - sagitttal flipped
`private short`	`unused1`	MIPAV uses this variable to define the X-axis orientation.
`private short`	`unused2`	MIPAV uses this variable to define the Y-axis orientation.
`private short`	`unused3`	MIPAV uses this variable to define the Z-axis orientation.
`private float`	`verified`	Unknown use.
`private int`	`views`	Unknown use.
`private int`	`vols_added`	Unknown use.
`private java.lang.String`	`vox_units`	specifies the spatial units of measure for a voxel.

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_STRING, XRAY_ANGIOGRAPHY

Constructor Summary

Constructors
Constructor Description

FileInfoAnalyze(java.lang.String name, java.lang.String directory, int format)
File info storage constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`displayAboutInfo(JDialogBase dlog, TransMatrix matrix)`	Displays the file information.
`java.lang.String`	`getAuxFile()`	Accessor to the aux_file string.
`short`	`getBitPix()`	Accessor to the bitpix value.
`float`	`getCalMax()`	Accessor to cal-max.
`float`	`getCalMin()`	Accessor to cal_min.
`java.lang.String`	`getCalUnits()`	Provides the string for cal units.
`float`	`getCompressed()`	Provides the compressed value.
`short`	`getDataTypeCode()`	Accessor to coded datatype value.
`java.lang.String`	`getDataTypeName()`	Accessor to the 10 character string of data-type.
`java.lang.String`	`getDBname()`	Accessor to DB_name.
`java.lang.String`	`getDescription()`	Accessor to the current analyze-image description.
`short`	`getDim()`	Accessor to the dim_un0.
`java.lang.String`	`getExperimentDate()`	Provides the current experiment date string.
`java.lang.String`	`getExperimentTime()`	Provides the current experiment time string.
`int`	`getFieldSkip()`	Provides the current field_skip value.
`int`	`getFileExtents()`	Analyze _extents_ value of 16,384.
`float`	`getFunused1()`	MIPAV hack to the ANALYZE standard.
`float`	`getFunused2()`	MIPAV hack to the ANALYZE standard.
`float`	`getFunused3()`	MIPAV hack to the ANALYZE standard.
`java.lang.String`	`getGenerated()`	Provides the current generated string.
`int`	`getGLmax()`	Provides the value of glmax.
`int`	`getGLmin()`	Provides the value of glmin.
`java.lang.String`	`getHist()`	Accessor to get the Analyze's hist_un0 string.
`char`	`getHkey()`	Accessor to get the Analyze's hkey_un0 string.
`int`	`getOmax()`	Provides current omax value.
`int`	`getOmin()`	Provides current omin value.
`byte`	`getOrientation()`	Provides the current orientation value.
`java.lang.String`	`getOriginator()`	Provides the current originator string.
`java.lang.String`	`getPatientID()`	Provides the current patient id.
`char`	`getRegular()`	Provides the value of regular character.
`java.lang.String`	`getScanNum()`	Provides the current scannum string.
`short`	`getSessionErr()`	Provide the value of session err.
`int`	`getSizeOfHeader()`	Provides the current scannum string.
`int`	`getSmax()`	Provides current smax value.
`int`	`getSmin()`	Provides current smin value.
`int`	`getStartField()`	Provides the current value for the start_field.
`short`	`getUnused1()`	provides current unused1 value.
`short`	`getUnused2()`	Provides current unused2 value.
`short`	`getUnused3()`	Provides current unused3 value.
`float`	`getVerified()`	Provides the verified value.
`int`	`getViews()`	Provides current views value.
`int`	`getVolsAdded()`	Provides the current vols_added value.
`java.lang.String`	`getVoxUnits()`	Provides the string for vox-units.
`private java.lang.String`	`selectOrientationText(int orientation)`	Selection of text for the table and the editpanel.
`void`	`setAuxFile(java.lang.String auxFile)`	Supplies auxiliary-file string; permits no more than 24 characters.
`void`	`setAxisOrientation(int[] axOrient)`	Sets orientation of each axis.
`void`	`setAxisOrientation(int axOrient, int axis)`	Sets the image orientation in the specified axis.
`void`	`setBitPix(short bp)`	Sets bitpix; any value other than 1, 8, 16, 32, 64, or 24 gets set to the dissalowed trap value, -1.
`void`	`setCalMax(float cal)`	sets cal-max. if supplied value is less than cal-min, the cal-min gets reset to the supplied value as well, so that cal-min is still no greater than cal-max.
`void`	`setCalMin(float cal)`	Sets cal-min. if supplied value is greater than cal-max, the cal-max gets reset to the supplied value as well, so that cal-max is still no less than cal-min.
`void`	`setCalUnits(java.lang.String cal)`	Allows no more than 8 characters for the string describing the cal units.
`void`	`setCompressed(float comp)`	sets the compressed variable.
`void`	`setDataType(short dtype)`	Accessor to supply coded datatype.
`void`	`setDataType(java.lang.String dtype)`	Permits 10 charactar large string for data-type.
`void`	`setDBname(java.lang.String dbname)`	Set the database name - limit 18 character max to set the DB_NAME value.
`void`	`setDescription(java.lang.String description)`	Allows no more than 80 characters to fill in the analyze-image description.
`void`	`setDim(short un0)`	DOCUMENT ME!
`void`	`setExperimentDate(java.lang.String date)`	Allows a maximum of 10 characters to set the experiment date string.
`void`	`setExperimentTime(java.lang.String time)`	Allows a maximum of 10 characters to set the experiment time string.
`void`	`setFieldSkip(int field)`	Supplies the submitted value to the field_sip variable.
`void`	`setFileExtents(int ext)`	DOCUMENT ME!
`void`	`setFunused1(float fun)`	Sets the start locations in the x-axis in fileInfoBase.
`void`	`setFunused2(float fun)`	Sets the start locations in the y-axis in fileInfoBase.
`void`	`setFunused3(float fun)`	Sets the start locations in the z-axis in fileInfoBase.
`void`	`setGenerated(java.lang.String gen)`	Allows a maximum of 10 characters to set the generated string.
`void`	`setGLmax(int gl)`	Sets glmax. if supplied value is less than glmin, the glmin gets reset to the supplied value as well, so that glmin is still no greater than glmax.
`void`	`setGLmin(int gl)`	Sets glmin. if supplied value is greater than glmax, the glmax gets reset to the supplied value as well, so that glmax is still no less than glmin.
`void`	`setHist(java.lang.String hist)`	DOCUMENT ME!
`void`	`setHkey(char hk)`	DOCUMENT ME!
`void`	`setOmax(int oMax)`	Sets omax.
`void`	`setOmin(int oMin)`	Sets omin. if supplied value is greater than omax, the omax gets reset to the supplied value as well, so that omax is still no less than omin.
`void`	`setOrientation(byte orientation)`	Sets the image orientation converting from analyze specific orientation to general orientation.
`void`	`setOrigin(float[] stlocat)`	Sets start locations of each axis.
`void`	`setOrigin(float fun, int axis)`	Sets the start location of the specified axis.
`void`	`setOriginator(java.lang.String originator)`	Allows a maximum of 10 characters to set the originator string.
`void`	`setPatientID(java.lang.String patIDnum)`	Allows a maximum of 10 characters to set the patient ID string.
`void`	`setRegular(char ch)`	Supply the value of regular character.
`void`	`setScanNum(java.lang.String scanNum)`	Allows a maximum of 10 characters to set the scannum string.
`void`	`setSessionErr(short sessionError)`	Supply the value of session error.
`void`	`setSizeOfHeader(int size)`	Sets the size of the header which is always 348.
`void`	`setSmax(int sMax)`	Sets smax.
`void`	`setSmin(int sMin)`	Sets smin.
`void`	`setStartField(int startField)`	Supplies the submitted value to the start_field variable.
`protected java.lang.String`	`setString(java.lang.String str, int length)`	Verifies string is not larger than length; strings larger than length, are clipped before being returned.
`void`	`setUnused1(int unused)`	Sets unused 1.
`void`	`setUnused2(int unused)`	Sets unused 2.
`void`	`setUnused3(int unused)`	Sets unused 3.
`void`	`setVerified(float verified)`	Supply the value to verified.
`void`	`setViews(int view)`	Sets the views variable.
`void`	`setVolsAdded(int vols)`	Supplies a value to the vols_added valiable.
`void`	`setVoxUnits(java.lang.String voxUnits)`	Allows no more than 4 characters for the string describing the vox units.
`void`	`stateChanged(java.util.Vector ce)`	.
`void`	`updateFileInfos(FileInfoAnalyze fInfo)`	Propogates the current file info to another FileInfoAnalyze except for the 3 start locations kept in funused1, funused2, funused3.

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, 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, 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
- DT_NONE
```
public static final short DT_NONE
```
  Analyze file format define use to indicate no image data type.
  
  See Also:
  
  Constant Field Values
- DT_UNKNOWN
```
public static final short DT_UNKNOWN
```
  AAnalyze file format define use to indicate undefined image data type.
  
  See Also:
  
  Constant Field Values
- DT_BINARY
```
public static final short DT_BINARY
```
  Analyze file format define use to indicate binary (1 bit) image data type.
  
  See Also:
  
  Constant Field Values
- DT_UNSIGNED_CHAR
```
public static final short DT_UNSIGNED_CHAR
```
  Analyze file format define use to indicate unsigned byte (char) (8 bit) image data type.
  
  See Also:
  
  Constant Field Values
- DT_SIGNED_SHORT
```
public static final short DT_SIGNED_SHORT
```
  Analyze file format define use to indicate short (16 bit) image data type.
  
  See Also:
  
  Constant Field Values
- DT_UNSIGNED_SHORT
```
public static final short DT_UNSIGNED_SHORT
```
  Analyze file format define use to indicate short (16 bit) image data type.
  
  See Also:
  
  Constant Field Values
- DT_SIGNED_INT
```
public static final short DT_SIGNED_INT
```
  Analyze file format define use to indicate integer (32 bit) image data type.
  
  See Also:
  
  Constant Field Values
- DT_FLOAT
```
public static final short DT_FLOAT
```
  Analyze file format define use to indicate float (32 bit) image data type.
  
  See Also:
  
  Constant Field Values
- DT_COMPLEX
```
public static final short DT_COMPLEX
```
  Analyze file format define use to indicate complex (64 bit) image data type.
  
  See Also:
  
  Constant Field Values
- DT_DOUBLE
```
public static final short DT_DOUBLE
```
  Analyze file format define use to indicate double (64 bit) image data type.
  
  See Also:
  
  Constant Field Values
- DT_RGB
```
public static final short DT_RGB
```
  Analyze file format define use to indicate color (RGB - 24 bits) image data type.
  
  See Also:
  
  Constant Field Values
- DT_ALL
```
public static final short DT_ALL
```
  Analyze file format define use to indicate _ALL_ image data type.
  
  See Also:
  
  Constant Field Values
- UNKNOWN_ORIENT
```
public static final byte UNKNOWN_ORIENT
```
  The data_history substructure is not required, but the orient element is used to indicate individual slice orientation and determines whetther the Analyze Movie program will attempt to flip the images before displaying a movie sequence. 0 - transverse unflipped 1 - coronal unflipped 2 - sagitttal unflipped 3 - transverse flipped 4 - coronal flipped 5 - sagitttal flipped
  
  See Also:
  
  Constant Field Values
- TRANSVERSE_UNFLIPPED
```
public static final byte TRANSVERSE_UNFLIPPED
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- CORONAL_UNFLIPPED
```
public static final byte CORONAL_UNFLIPPED
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- SAGITTAL_UNFLIPPED
```
public static final byte SAGITTAL_UNFLIPPED
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- TRANSVERSE_FLIPPED
```
public static final byte TRANSVERSE_FLIPPED
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- CORONAL_FLIPPED
```
public static final byte CORONAL_FLIPPED
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- SAGITTAL_FLIPPED
```
public static final byte SAGITTAL_FLIPPED
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- aux_file
```
private java.lang.String aux_file
```
  DOCUMENT ME!
- bitpix
```
private short bitpix
```
  Bits per pixel. Valid values include: 1, 8, 16, 32, 64, 24(rgb).
- cal_max
```
private float cal_max
```
  Range of calibration values.
- cal_min
```
private float cal_min
```
  Values of 0.0 for both fields imply that no calibration min and max values are used !
- cal_units
```
private java.lang.String cal_units
```
  Specifies the name of the calibration unit.
- compressed
```
private float compressed
```
  Indicates if compression is used. Default is -1 indicating no compression
- data_type
```
private java.lang.String data_type
```
  Unknown use 10 chars.
- datatype
```
private short datatype
```
  Stores the image data type DT_NONE = 0; DT_UNKNOWN = 0; DT_BINARY = 1; DT_UNSIGNED_CHAR = 2; DT_SIGNED_SHORT = 4; DT_UNSIGNED_SHORT = 4; DT_SIGNED_INT = 8; DT_FLOAT = 16; DT_COMPLEX = 32; DT_DOUBLE = 64; DT_RGB = 128; DT_ALL = 255;
- db_name
```
private java.lang.String db_name
```
  Name of file with a length of 18 chars.
- descrip
```
private java.lang.String descrip
```
  String with a max character length of 80 used to describe image.
- dim_un0
```
private short dim_un0
```
  Unused.
- exp_date
```
private java.lang.String exp_date
```
  String with a max character length of 10 used to indicate the experiment date.
- exp_time
```
private java.lang.String exp_time
```
  String with a max character length of 10 used to indicate the experiment time.
- extents
```
private int extents
```
  Should be 16384.
- field_skip
```
private int field_skip
```
  Unknown length.
- funused1
```
private float funused1
```
  MIPAV uses this variable to define the X-axis origin.
- funused2
```
private float funused2
```
  MIPAV uses this variable to define the Y-axis origin.
- funused3
```
private float funused3
```
  MIPAV uses this variable to define the Z-axis origin.
- generated
```
private java.lang.String generated
```
  Unknown use. Length of 10.
- glmax
```
private int glmax
```
  Maximum pixel values for the entire dataset.
- glmin
```
private int glmin
```
  Minimum pixel values for the entire database.
- hist_un0
```
private java.lang.String hist_un0
```
  Unknown use. Length of 3.
- hkey_un0
```
private char hkey_un0
```
  Unknown use. Length of 1.
- omax
```
private int omax
```
  Unknown use.
- omin
```
private int omin
```
  Unknown use.
- orient
```
private byte orient
```
  DOCUMENT ME!
- originator
```
private java.lang.String originator
```
  Unknown use. Length of 10.
- patient_id
```
private java.lang.String patient_id
```
  Patient's ID. Length of 10.
- regular
```
private char regular
```
  I think it means data has uniform spacing (resolutions).
- scannum
```
private java.lang.String scannum
```
  Scan ID Length of 10.
- session_error
```
private short session_error
```
  Unknown use.
- sizeof_hdr
```
private int sizeof_hdr
```
  Always of length 348.
- smax
```
private int smax
```
  Unknown use.
- smin
```
private int smin
```
  Unknown use.
- start_field
```
private int start_field
```
  Unknown use.
- unused1
```
private short unused1
```
  MIPAV uses this variable to define the X-axis orientation.
- unused2
```
private short unused2
```
  MIPAV uses this variable to define the Y-axis orientation.
- unused3
```
private short unused3
```
  MIPAV uses this variable to define the Z-axis orientation.
- verified
```
private float verified
```
  Unknown use.
- views
```
private int views
```
  Unknown use.
- vols_added
```
private int vols_added
```
  Unknown use.
- vox_units
```
private java.lang.String vox_units
```
  specifies the spatial units of measure for a voxel.

Constructor Detail

FileInfoAnalyze

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

File info storage constructor.

Parameters:: name - file name; directory - directory; format - file format

Method Detail

displayAboutInfo
```
public void displayAboutInfo(JDialogBase dlog,
                             TransMatrix matrix)
```
Displays the file information.

Specified by:

displayAboutInfo in class FileInfoBase

Parameters:

dlog - dialog box that is written to

matrix - transformation matrix

getAuxFile
```
public java.lang.String getAuxFile()
```
Accessor to the aux_file string.

Returns:

String aux_file

getBitPix
```
public short getBitPix()
```
Accessor to the bitpix value.

Returns:

short the bitpix value.

getCalMax
```
public float getCalMax()
```
Accessor to cal-max.

Returns:

float cal_max

getCalMin
```
public float getCalMin()
```
Accessor to cal_min.

Returns:

float cal_min

getCalUnits
```
public java.lang.String getCalUnits()
```
Provides the string for cal units.

Returns:

String string for cal_units

getCompressed
```
public float getCompressed()
```
Provides the compressed value.

Returns:

float compressed

getDataTypeCode
```
public short getDataTypeCode()
```
Accessor to coded datatype value.

Returns:

short datatype

getDataTypeName
```
public java.lang.String getDataTypeName()
```
Accessor to the 10 character string of data-type.

Returns:

String returns data_type

getDBname
```
public java.lang.String getDBname()
```
Accessor to DB_name.

Returns:

String database name

getDescription
```
public java.lang.String getDescription()
```
Accessor to the current analyze-image description.

Returns:

String description

getDim
```
public short getDim()
```
Accessor to the dim_un0.

Returns:

Returns the dim_un0 variable.

getExperimentDate
```
public java.lang.String getExperimentDate()
```
Provides the current experiment date string.

Returns:

String the experiment date.

getExperimentTime
```
public java.lang.String getExperimentTime()
```
Provides the current experiment time string.

Returns:

String the experiment time

getFieldSkip
```
public int getFieldSkip()
```
Provides the current field_skip value.

Returns:

int the field_skip value

getFileExtents
```
public int getFileExtents()
```
Analyze _extents_ value of 16,384.

Returns:

The extents value which always seems to be 16,384.

getFunused1
```
public float getFunused1()
```
MIPAV hack to the ANALYZE standard. Retrieves start locaiton from x-axis. To be stored as Funused1.

Returns:

float funused1

getFunused2
```
public float getFunused2()
```
MIPAV hack to the ANALYZE standard. Retrieves start locaiton from y-axis. To be stored as Funused2.

Returns:

float funused2

getFunused3
```
public float getFunused3()
```
MIPAV hack to the ANALYZE standard. Retrieves start location from z-axis. To be stored as Funused3.

Returns:

float funused3

getGenerated
```
public java.lang.String getGenerated()
```
Provides the current generated string.

Returns:

String generated string

getGLmax
```
public int getGLmax()
```
Provides the value of glmax.

Returns:

int glmax

getGLmin
```
public int getGLmin()
```
Provides the value of glmin.

Returns:

int glmin

getHist
```
public java.lang.String getHist()
```
Accessor to get the Analyze's hist_un0 string.

Returns:

Returns the hist_un0 string.

getHkey
```
public char getHkey()
```
Accessor to get the Analyze's hkey_un0 string.

Returns:

Returns the hkey_un0 string.

getOmax
```
public int getOmax()
```
Provides current omax value.

Returns:

int the omax value

getOmin
```
public int getOmin()
```
Provides current omin value.

Returns:

int the omin value

getOrientation
```
public byte getOrientation()
```
Provides the current orientation value.

Returns:

byte orientation value

getOriginator
```
public java.lang.String getOriginator()
```
Provides the current originator string.

Returns:

String originator string

getPatientID
```
public java.lang.String getPatientID()
```
Provides the current patient id.

Returns:

String the patient id

getRegular
```
public char getRegular()
```
Provides the value of regular character.

Returns:

char value of regular character

getScanNum
```
public java.lang.String getScanNum()
```
Provides the current scannum string.

Returns:

String current scannum string

getSessionErr
```
public short getSessionErr()
```
Provide the value of session err.

Returns:

short session_error

getSizeOfHeader
```
public int getSizeOfHeader()
```
Provides the current scannum string.

Returns:

String current scannum string

getSmax
```
public int getSmax()
```
Provides current smax value.

Returns:

int the smax value

getSmin
```
public int getSmin()
```
Provides current smin value.

Returns:

int the smin value

getStartField
```
public int getStartField()
```
Provides the current value for the start_field.

Returns:

int the start_field

getUnused1
```
public short getUnused1()
```
provides current unused1 value.

Returns:

short unused1 value

getUnused2
```
public short getUnused2()
```
Provides current unused2 value.

Returns:

short unused2 value

getUnused3
```
public short getUnused3()
```
Provides current unused3 value.

Returns:

short unused3 value

getVerified
```
public float getVerified()
```
Provides the verified value.

Returns:

The Analyze verified parameter.

getViews
```
public int getViews()
```
Provides current views value.

Returns:

The view parameter.

getVolsAdded
```
public int getVolsAdded()
```
Provides the current vols_added value.

Returns:

The vols_added

getVoxUnits
```
public java.lang.String getVoxUnits()
```
Provides the string for vox-units.

Returns:

The vox_units parameter

setAuxFile
```
public void setAuxFile(java.lang.String auxFile)
```
Supplies auxiliary-file string; permits no more than 24 characters.

Parameters:

auxFile - T

setAxisOrientation
```
public void setAxisOrientation(int[] axOrient)
```
Sets orientation of each axis.

Overrides:

setAxisOrientation in class FileInfoBase

Parameters:

axOrient - axis orientation array

See Also:

FileInfoBase.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.

Overrides:

setAxisOrientation in class FileInfoBase

Parameters:

axOrient - orientation

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

setBitPix
```
public void setBitPix(short bp)
```
Sets bitpix; any value other than 1, 8, 16, 32, 64, or 24 gets set to the dissalowed trap value, -1.

Parameters:

bp - DOCUMENT ME!

setCalMax
```
public void setCalMax(float cal)
```
sets cal-max. if supplied value is less than cal-min, the cal-min gets reset to the supplied value as well, so that cal-min is still no greater than cal-max.

Parameters:

cal - DOCUMENT ME!

setCalMin
```
public void setCalMin(float cal)
```
Sets cal-min. if supplied value is greater than cal-max, the cal-max gets reset to the supplied value as well, so that cal-max is still no less than cal-min.

Parameters:

cal - DOCUMENT ME!

setCalUnits
```
public void setCalUnits(java.lang.String cal)
```
Allows no more than 8 characters for the string describing the cal units.

Parameters:

cal - DOCUMENT ME!

setCompressed
```
public void setCompressed(float comp)
```
sets the compressed variable.

Parameters:

comp - DOCUMENT ME!

setDataType
```
public void setDataType(java.lang.String dtype)
```
Permits 10 charactar large string for data-type.

Parameters:

dtype - DOCUMENT ME!

setDataType
```
public void setDataType(short dtype)
```
Accessor to supply coded datatype.

Parameters:

dtype - DOCUMENT ME!

setDBname
```
public void setDBname(java.lang.String dbname)
```
Set the database name - limit 18 character max to set the DB_NAME value.

Parameters:

dbname - DOCUMENT ME!

setDescription
```
public void setDescription(java.lang.String description)
```
Allows no more than 80 characters to fill in the analyze-image description.

Parameters:

description - DOCUMENT ME!

setDim
```
public void setDim(short un0)
```
DOCUMENT ME!

Parameters:

un0 - DOCUMENT ME!

setExperimentDate
```
public void setExperimentDate(java.lang.String date)
```
Allows a maximum of 10 characters to set the experiment date string.

Parameters:

date - DOCUMENT ME!

setExperimentTime
```
public void setExperimentTime(java.lang.String time)
```
Allows a maximum of 10 characters to set the experiment time string.

Parameters:

time - DOCUMENT ME!

setFieldSkip
```
public void setFieldSkip(int field)
```
Supplies the submitted value to the field_sip variable.

Parameters:

field - DOCUMENT ME!

setFileExtents
```
public void setFileExtents(int ext)
```
DOCUMENT ME!

Parameters:

ext - DOCUMENT ME!

setFunused1
```
public void setFunused1(float fun)
```
Sets the start locations in the x-axis in fileInfoBase. This is a hack into the ANALYZE standard to compensate for start locations not being known. To be Stored in the Funused1 variable.

Parameters:

fun - x start location

See Also:

FileInfoBase#setStartLocations(float, int)

setFunused2
```
public void setFunused2(float fun)
```
Sets the start locations in the y-axis in fileInfoBase. This is a hack into the ANALYZE standard to compensate for start locations not being known. To be Stored in the Funused2 variable.

Parameters:

fun - y start location

See Also:

FileInfoBase#setStartLocations(float, int)

setFunused3
```
public void setFunused3(float fun)
```
Sets the start locations in the z-axis in fileInfoBase. This is a hack into the ANALYZE standard to compensate for start locations not being known. To be Stored in the Funused3 variable.

Parameters:

fun - z start location

setGenerated
```
public void setGenerated(java.lang.String gen)
```
Allows a maximum of 10 characters to set the generated string.

Parameters:

gen - DOCUMENT ME!

setGLmax
```
public void setGLmax(int gl)
```
Sets glmax. if supplied value is less than glmin, the glmin gets reset to the supplied value as well, so that glmin is still no greater than glmax.

Parameters:

gl - DOCUMENT ME!

setGLmin
```
public void setGLmin(int gl)
```
Sets glmin. if supplied value is greater than glmax, the glmax gets reset to the supplied value as well, so that glmax is still no less than glmin.

Parameters:

gl - DOCUMENT ME!

setHist

public void setHist(java.lang.String hist)

DOCUMENT ME!

Parameters:: hist - DOCUMENT ME!

setHkey
```
public void setHkey(char hk)
```
DOCUMENT ME!

Parameters:

hk - DOCUMENT ME!

setOmax
```
public void setOmax(int oMax)
```
Sets omax. If supplied value is less than omin, the omin gets reset to the supplied value as well, so that omin is still no greater than omax.

Parameters:

oMax - Value that omax is set to.

setOmin
```
public void setOmin(int oMin)
```
Sets omin. if supplied value is greater than omax, the omax gets reset to the supplied value as well, so that omax is still no less than omin.

Parameters:

oMin - Value that omin is set to.

setOrientation
```
public void setOrientation(byte orientation)
```
Sets the image orientation converting from analyze specific orientation to general orientation. Value may be transverse, coronal, or sagittal.
see the top of this document for all possible values. supplying a value other than one of these 6 possiblities sets the orientation to an impossible 'flag' value.

See Also:

FileInfoBase.setImageOrientation(int)

setOrigin
```
public void setOrigin(float[] stlocat)
```
Sets start locations of each axis.

Overrides:

setOrigin in class FileInfoBase

Parameters:

stlocat - axis start location array

See Also:

FileInfoBase#getStartLocations()

setOrigin
```
public void setOrigin(float fun,
                      int axis)
```
Sets the start location of the specified axis.

Overrides:

setOrigin in class FileInfoBase

Parameters:

fun - origin coord.

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

See Also:

#getStartLocations(int)

setOriginator
```
public void setOriginator(java.lang.String originator)
```
Allows a maximum of 10 characters to set the originator string.

Parameters:

originator - Originator string.

setPatientID
```
public void setPatientID(java.lang.String patIDnum)
```
Allows a maximum of 10 characters to set the patient ID string.

Parameters:

patIDnum - Patient ID string.

setRegular
```
public void setRegular(char ch)
```
Supply the value of regular character.

Parameters:

ch - value of r indicates all images are of the same size which seems to always be the case.

setScanNum
```
public void setScanNum(java.lang.String scanNum)
```
Allows a maximum of 10 characters to set the scannum string.

Parameters:

scanNum - Scan number of the image.

setSessionErr
```
public void setSessionErr(short sessionError)
```
Supply the value of session error.

Parameters:

sessionError - The session error.

setSizeOfHeader
```
public void setSizeOfHeader(int size)
```
Sets the size of the header which is always 348.

Parameters:

size - The size of the header which is always 348 for Analyze images.

setSmax
```
public void setSmax(int sMax)
```
Sets smax. If supplied value is less than smin, the smin gets reset to the supplied value as well, so that smin is still no greater than smax.

Parameters:

sMax - DOCUMENT ME!

setSmin
```
public void setSmin(int sMin)
```
Sets smin. If supplied value is greater than smax, the smax gets reset to the supplied value as well, so that smax is still no less than smin.

Parameters:

sMin - The sMin value.

setStartField
```
public void setStartField(int startField)
```
Supplies the submitted value to the start_field variable.

Parameters:

startField - The start field value.

setUnused1
```
public void setUnused1(int unused)
```
Sets unused 1.

Parameters:

unused - The unused value.

setUnused2
```
public void setUnused2(int unused)
```
Sets unused 2.

Parameters:

unused - The unused value.

setUnused3
```
public void setUnused3(int unused)
```
Sets unused 3.

Parameters:

unused - The unused value.

setVerified
```
public void setVerified(float verified)
```
Supply the value to verified.

Parameters:

verified - The verified value

setViews
```
public void setViews(int view)
```
Sets the views variable.

Parameters:

view - The view value.

setVolsAdded
```
public void setVolsAdded(int vols)
```
Supplies a value to the vols_added valiable.

Parameters:

vols - DOCUMENT ME!

setVoxUnits
```
public void setVoxUnits(java.lang.String voxUnits)
```
Allows no more than 4 characters for the string describing the vox units.

Parameters:

voxUnits - DOCUMENT ME!

stateChanged

public void stateChanged(java.util.Vector ce)

.

ce[0] = table	0 = primary, 1 = secondary, etC
ce[1] = line of table
ce[2] = string name	eg, "Type"
ce[3] = Vector codeValue	eg, "B"
ce[4] = string value	eg, "Big"

"ce" comes from ChangeEvent upon which this is based. care to make our own ChangeEvent to store and handle this?

Parameters:: ce - DOCUMENT ME!

updateFileInfos
```
public void updateFileInfos(FileInfoAnalyze fInfo)
```
Propogates the current file info to another FileInfoAnalyze except for the 3 start locations kept in funused1, funused2, funused3.
It does not copy over the datatypeCode. (though, aside from, "it isn't in the about table", I can't think of a reason why it shouldn't. but it doesn't.) Also, copied over is bitPix, aux_file.

Some variables, such as the unused1, unused2, unused3, are really taken from unused, rather than from the start locations as we are re-using the funused variables. This means that if the unused variables are not right to begin with, this certainly won't correct them!

Parameters:

fInfo - File info. object used to update values in this object.

setString
```
protected java.lang.String setString(java.lang.String str,
                                     int length)
```
Verifies string is not larger than length; strings larger than length, are clipped before being returned.

Parameters:

str - The input string.

length - The maximum length of the string.

Returns:

String new substring

selectOrientationText
```
private java.lang.String selectOrientationText(int orientation)
```
Selection of text for the table and the editpanel.

Parameters:

orientation - value indicating the orientation.

Returns:

String the orientation string

Class FileInfoAnalyze

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

DT_NONE

DT_UNKNOWN

DT_BINARY

DT_UNSIGNED_CHAR

DT_SIGNED_SHORT

DT_UNSIGNED_SHORT

DT_SIGNED_INT

DT_FLOAT

DT_COMPLEX

DT_DOUBLE

DT_RGB

DT_ALL

UNKNOWN_ORIENT

TRANSVERSE_UNFLIPPED

CORONAL_UNFLIPPED

SAGITTAL_UNFLIPPED

TRANSVERSE_FLIPPED

CORONAL_FLIPPED

SAGITTAL_FLIPPED

aux_file

bitpix

cal_max

cal_min

cal_units

compressed

data_type

datatype

db_name

descrip

dim_un0

exp_date

exp_time

extents

field_skip

funused1

funused2

funused3

generated

glmax

glmin

hist_un0

hkey_un0

omax

omin

orient

originator

patient_id

regular

scannum

session_error

sizeof_hdr

smax

smin

start_field

unused1

unused2

unused3

verified

views

vols_added

vox_units

Constructor Detail

FileInfoAnalyze

Method Detail

displayAboutInfo

getAuxFile

getBitPix

getCalMax