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

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable
```
public class FileInfoSPM
extends FileInfoBase
```
This structures contains the information that describes how an SPM image is stored on disk. We have extended this format to store image orientation and start locations. 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.
Differences between MIPAV ANALYZE and SPM: In MIPAV ANALYZE we have location 60 cal_units 4 unsigned characters location 64 - X-axis orientation @see FileInfoBase for static variables that are set. location 66 - Y-axis orientation // All three unused variables are of short type. location 68 - Z-axis orientation In SPM we have location 60 cal_units 8 unsigned characters location 68 unused1

In MIPAV ANALYZE we have location 112 Funused1 - X-axis starting location (origin from upper left-hand corner) location 116 Funused2 - Y-axis starting location (origin from upper left-hand corner) location 120 Funused3 - Z-axis starting location (origin is the first image slice) In SPM we have location 112 Funused1 scale a floating point scale factor applied during memory mapping location 116 Funused2 location 120 Funused3

In MIPAV ANALYZE we have location 253 originator with 10 characters In SPM we have location 253 origin with 5 shorts. If the first 3 shorts of a 3D image are set to 0, 0, 0, the origin is assumed to be at the center of the volume, since in SPM the corner voxel is at 1, 1, 1. The position(x,y,z) in mm. is determined by the distance(x,y,z) from the origin multiplied by the vox_units(x,y,z).

In SPM the signed byte datatype was added with DT_BYTE = 130. MIPAV ANALYZE uses UNSIGNED_SHORT = 6 while SPM uses DT_UNSIGNED_SHORT = 132. The SPM standard also provides for an unsigned int = 136, but MIPAV does not used the unsigned int data type. Note that in SPM while DATA = datatype * 256 for swapped bytes, only datatype and not DATA is written to the file, so in this program we need never consider the multiplicative factors of 256.

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

Version:

1.0 July, 2002

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

FileSPM, 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`	DOCUMENT ME!
`private float`	`cal_max`	DOCUMENT ME!
`private float`	`cal_min`	DOCUMENT ME!
`private java.lang.String`	`cal_units`	DOCUMENT ME!
`private float`	`compressed`	DOCUMENT ME!
`static byte`	`CORONAL_FLIPPED`	DOCUMENT ME!
`static byte`	`CORONAL_UNFLIPPED`	DOCUMENT ME!
`private java.lang.String`	`data_type`	DOCUMENT ME!
`private short`	`datatype`	DOCUMENT ME!
`private java.lang.String`	`db_name`	DOCUMENT ME!
`private java.lang.String`	`descrip`	DOCUMENT ME!
`private short`	`dim_un0`	DOCUMENT ME!
`static int`	`DT_ALL`	DOCUMENT ME!
`static int`	`DT_BINARY`	DOCUMENT ME!
`static int`	`DT_BYTE`	DOCUMENT ME!
`static int`	`DT_COMPLEX`	DOCUMENT ME!
`static int`	`DT_DOUBLE`	DOCUMENT ME!
`static int`	`DT_FLOAT`	DOCUMENT ME!
`static int`	`DT_NONE`	DOCUMENT ME!
`static int`	`DT_RGB`	DOCUMENT ME!
`static int`	`DT_SIGNED_INT`	DOCUMENT ME!
`static int`	`DT_SIGNED_SHORT`	DOCUMENT ME!
`static int`	`DT_UNKNOWN`	DOCUMENT ME!
`static int`	`DT_UNSIGNED_CHAR`	DOCUMENT ME!
`static int`	`DT_UNSIGNED_INT`	DOCUMENT ME!
`static int`	`DT_UNSIGNED_SHORT`	DOCUMENT ME!
`private java.lang.String`	`exp_date`	DOCUMENT ME!
`private java.lang.String`	`exp_time`	DOCUMENT ME!
`private int`	`extents`	DOCUMENT ME!
`private int`	`field_skip`	DOCUMENT ME!
`private java.lang.String`	`generated`	DOCUMENT ME!
`private int`	`glmax`	DOCUMENT ME!
`private int`	`glmin`	DOCUMENT ME!
`private java.lang.String`	`hist_un0`	DOCUMENT ME!
`private char`	`hkey_un0`	DOCUMENT ME!
`private int`	`omax`	DOCUMENT ME!
`private int`	`omin`	DOCUMENT ME!
`private byte`	`orient`	DOCUMENT ME!
`private short[]`	`origin`	DOCUMENT ME!
`private java.lang.String`	`patient_id`	DOCUMENT ME!
`private char`	`regular`	DOCUMENT ME!
`static byte`	`SAGITTAL_FLIPPED`	DOCUMENT ME!
`static byte`	`SAGITTAL_UNFLIPPED`	DOCUMENT ME!
`private float`	`scale`	a floating point scale factor used during memory mapping.
`private java.lang.String`	`scannum`	DOCUMENT ME!
`private static long`	`serialVersionUID`	Use serialVersionUID for interoperability.
`private short`	`session_error`	DOCUMENT ME!
`private int`	`sizeof_hdr`	DOCUMENT ME!
`private int`	`smax`	DOCUMENT ME!
`private int`	`smin`	DOCUMENT ME!
`private int`	`start_field`	DOCUMENT ME!
`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 SPM 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 float`	`verified`	DOCUMENT ME!
`private int`	`views`	DOCUMENT ME!
`private int`	`vols_added`	DOCUMENT ME!
`private float`	`vox_offset`	public float pixdim = new float[8]; // image resolutions info mm or ms stored in FileInfoBase pixdim[0] = number of dimensions pixdim[1] = voxel width pixdim[2] = voxel height pixdim[3] = voxel thickness pixdim[4] = time.
`private java.lang.String`	`vox_units`	public short dim[] = new short[8]; // image dimension data stored in FileInfoBase dim[0] = number of dimensions; usally 4 dim[1] = image width dim[2] = image height dim[3] = image depth (# of slices) dim[4] = volumes in image --- must be one for 3D image.

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, 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

FileInfoSPM(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 SPM-image description.
`short`	`getDim()`	DOCUMENT ME!
`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()`	DOCUMENT ME!
`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()`	DOCUMENT ME!
`char`	`getHkey()`	DOCUMENT ME!
`int`	`getOmax()`	provides current omax value.
`int`	`getOmin()`	provides current omin value.
`byte`	`getOrientation()`	provides the current orientation value.
`short[]`	`getOriginLoc()`	DOCUMENT ME!
`java.lang.String`	`getPatientID()`	provides the current patient id.
`char`	`getRegular()`	provides the value of regular character.
`float`	`getScale()`	DOCUMENT ME!
`java.lang.String`	`getScanNum()`	provides the current scannum string.
`short`	`getSessionErr()`	provide the value of session err.
`int`	`getSizeOfHeader()`	DOCUMENT ME!
`int`	`getSmax()`	provides current smax value.
`int`	`getSmin()`	provides current smin value.
`int`	`getStartField()`	provides the current value for the start_field.
`float`	`getVerified()`	provides the verified value.
`int`	`getViews()`	provides current views value.
`int`	`getVolsAdded()`	provides the current vols_added value.
`float`	`getVoxOffset()`	accessor to the vox offset value.
`java.lang.String`	`getVoxUnits()`	provides the string for vox-units.
`private java.lang.String`	`selectOrientationText(int or)`	selection of text for the table and the editpanel.
`void`	`setAuxFile(java.lang.String aux)`	supplies auxiliary-file string; permits no more than 24 characters.
`void`	`setAxisOrientation(int[] axOrient)`	Sets orientation of each 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)`	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 SPM-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`	`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`	`setMipavOrigin(float[] mipavOrigin)`
`void`	`setOmax(int o)`	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.
`void`	`setOmin(int o)`	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 SPM specific orientation to general orientation.
`void`	`setOrigin(short[] origin)`	DOCUMENT ME!
`void`	`setPatientID(java.lang.String IDnum)`	allows a maximum of 10 characters to set the patient ID string.
`void`	`setRegular(char ch)`	supply the value of regular character.
`void`	`setScale(float scale)`	DOCUMENT ME!
`void`	`setScanNum(java.lang.String num)`	allows a maximum of 10 characters to set the scannum string.
`void`	`setSessionErr(short s)`	supply the value of session error.
`void`	`setSizeOfHeader(int size)`	DOCUMENT ME!
`void`	`setSmax(int s)`	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.
`void`	`setSmin(int s)`	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.
`void`	`setStartField(int field)`	supplies the submitted value to the start_field variable.
`protected java.lang.String`	`setString(java.lang.String str, int len)`	verifies string is not larger than len length; strings larger than len, are clipped before being returned.
`void`	`setVerified(float veri)`	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`	`setVoxOffset(float vox)`	sets vox offset value.
`void`	`setVoxUnits(java.lang.String vox)`	allows no more than 4 characters for the string describing the vox units.
`void`	`stateChanged(java.util.Vector ce)`	.
`void`	`updateFileInfos(FileInfoSPM fInfo)`	Propogates the current file info to another FileInfoSPM 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, setAxisOrientation, setCameraMake, setCameraModel, setCompressionType, setDataType, setEndianess, setExposureTime, setExtents, setExtents, setFileDirectory, setFileFormat, setFileName, setFileSuffix, setFNumber, setFocalLength, setFocalLength35, setImageOrientation, setISOSpeedRating, setLUT, setMax, setMaxB, setMaxG, setMaxR, setMin, setMinB, setMinG, setMinR, setModality, setMultiFile, setOffset, setOrigin, setOrigin, setOriginalEndianess, setPhotometric, setPixelPadValue, setRescaleIntercept, setRescaleSlope, setResolutions, setResolutions, setSliceThickness, setTagDescription, setTagName, setUnitsOfMeasure, setUnitsOfMeasure, setUnitsOfMeasure, setUnitsOfMeasure, toString

Methods inherited from class gov.nih.mipav.model.structures.ModelSerialCloneable
clone, nativeClone

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail
- serialVersionUID
```
private static final long serialVersionUID
```
  Use serialVersionUID for interoperability.
  
  See Also:
  
  Constant Field Values
- DT_NONE
```
public static final int DT_NONE
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_UNKNOWN
```
public static final int DT_UNKNOWN
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_BINARY
```
public static final int DT_BINARY
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_BYTE
```
public static final int DT_BYTE
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_UNSIGNED_CHAR
```
public static final int DT_UNSIGNED_CHAR
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_SIGNED_SHORT
```
public static final int DT_SIGNED_SHORT
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_UNSIGNED_SHORT
```
public static final int DT_UNSIGNED_SHORT
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_SIGNED_INT
```
public static final int DT_SIGNED_INT
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_UNSIGNED_INT
```
public static final int DT_UNSIGNED_INT
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_FLOAT
```
public static final int DT_FLOAT
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_COMPLEX
```
public static final int DT_COMPLEX
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_DOUBLE
```
public static final int DT_DOUBLE
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_RGB
```
public static final int DT_RGB
```
  DOCUMENT ME!
  
  See Also:
  
  Constant Field Values
- DT_ALL
```
public static final int DT_ALL
```
  DOCUMENT ME!
  
  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 SPM 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
```
  DOCUMENT ME!
- cal_max
```
private float cal_max
```
  DOCUMENT ME!
- cal_min
```
private float cal_min
```
  DOCUMENT ME!
- cal_units
```
private java.lang.String cal_units
```
  DOCUMENT ME!
- compressed
```
private float compressed
```
  DOCUMENT ME!
- data_type
```
private java.lang.String data_type
```
  DOCUMENT ME!
- datatype
```
private short datatype
```
  DOCUMENT ME!
- db_name
```
private java.lang.String db_name
```
  DOCUMENT ME!
- descrip
```
private java.lang.String descrip
```
  DOCUMENT ME!
- dim_un0
```
private short dim_un0
```
  DOCUMENT ME!
- exp_date
```
private java.lang.String exp_date
```
  DOCUMENT ME!
- exp_time
```
private java.lang.String exp_time
```
  DOCUMENT ME!
- extents
```
private int extents
```
  DOCUMENT ME!
- field_skip
```
private int field_skip
```
  DOCUMENT ME!
- generated
```
private java.lang.String generated
```
  DOCUMENT ME!
- glmax
```
private int glmax
```
  DOCUMENT ME!
- glmin
```
private int glmin
```
  DOCUMENT ME!
- hist_un0
```
private java.lang.String hist_un0
```
  DOCUMENT ME!
- hkey_un0
```
private char hkey_un0
```
  DOCUMENT ME!
- omax
```
private int omax
```
  DOCUMENT ME!
- omin
```
private int omin
```
  DOCUMENT ME!
- orient
```
private byte orient
```
  DOCUMENT ME!
- origin
```
private short[] origin
```
  DOCUMENT ME!
- patient_id
```
private java.lang.String patient_id
```
  DOCUMENT ME!
- regular
```
private char regular
```
  DOCUMENT ME!
- scale
```
private float scale
```
  a floating point scale factor used during memory mapping.
- scannum
```
private java.lang.String scannum
```
  DOCUMENT ME!
- session_error
```
private short session_error
```
  DOCUMENT ME!
- sizeof_hdr
```
private int sizeof_hdr
```
  DOCUMENT ME!
- smax
```
private int smax
```
  DOCUMENT ME!
- smin
```
private int smin
```
  DOCUMENT ME!
- start_field
```
private int start_field
```
  DOCUMENT ME!
- verified
```
private float verified
```
  DOCUMENT ME!
- views
```
private int views
```
  DOCUMENT ME!
- vols_added
```
private int vols_added
```
  DOCUMENT ME!
- vox_offset
```
private float vox_offset
```
  public float pixdim = new float[8]; // image resolutions info mm or ms stored in FileInfoBase pixdim[0] = number of dimensions pixdim[1] = voxel width pixdim[2] = voxel height pixdim[3] = voxel thickness pixdim[4] = time.
- vox_units
```
private java.lang.String vox_units
```
  public short dim[] = new short[8]; // image dimension data stored in FileInfoBase dim[0] = number of dimensions; usally 4 dim[1] = image width dim[2] = image height dim[3] = image depth (# of slices) dim[4] = volumes in image --- must be one for 3D image.

Constructor Detail

FileInfoSPM

public FileInfoSPM(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 SPM-image description.

Returns:

String description

getDim
```
public short getDim()
```
DOCUMENT ME!

Returns:

DOCUMENT ME!

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()
```
DOCUMENT ME!

Returns:

DOCUMENT ME!

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()
```
DOCUMENT ME!

Returns:

DOCUMENT ME!

getHkey
```
public char getHkey()
```
DOCUMENT ME!

Returns:

DOCUMENT ME!

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

getOriginLoc
```
public short[] getOriginLoc()
```
DOCUMENT ME!

Returns:

origin

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

getScale
```
public float getScale()
```
DOCUMENT ME!

Returns:

float scale

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()
```
DOCUMENT ME!

Returns:

DOCUMENT ME!

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

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

Returns:

float verified

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

Returns:

int the view

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

Returns:

int the vols_added

getVoxOffset
```
public float getVoxOffset()
```
accessor to the vox offset value.

Returns:

float vox_offset

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

Returns:

String string for vox_units

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

Parameters:

aux - DOCUMENT ME!

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()

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)
```
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 SPM-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!

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 o)
```
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:

o - DOCUMENT ME!

setOmin
```
public void setOmin(int o)
```
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:

o - DOCUMENT ME!

setOrientation
```
public void setOrientation(byte orientation)
```
Sets the image orientation converting from SPM 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(short[] origin)
```
DOCUMENT ME!

Parameters:

origin - DOCUMENT ME!

setMipavOrigin

public void setMipavOrigin(float[] mipavOrigin)

Parameters:: mipavOrigin -

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

Parameters:

IDnum - DOCUMENT ME!

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

Parameters:

ch - DOCUMENT ME!

setScale
```
public void setScale(float scale)
```
DOCUMENT ME!

Parameters:

scale - DOCUMENT ME!

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

Parameters:

num - DOCUMENT ME!

setSessionErr
```
public void setSessionErr(short s)
```
supply the value of session error.

Parameters:

s - DOCUMENT ME!

setSizeOfHeader
```
public void setSizeOfHeader(int size)
```
DOCUMENT ME!

Parameters:

size - DOCUMENT ME!

setSmax
```
public void setSmax(int s)
```
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:

s - DOCUMENT ME!

setSmin
```
public void setSmin(int s)
```
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:

s - DOCUMENT ME!

setStartField
```
public void setStartField(int field)
```
supplies the submitted value to the start_field variable.

Parameters:

field - DOCUMENT ME!

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

Parameters:

veri - DOCUMENT ME!

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

Parameters:

view - DOCUMENT ME!

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

Parameters:

vols - DOCUMENT ME!

setVoxOffset
```
public void setVoxOffset(float vox)
```
sets vox offset value.

Parameters:

vox - DOCUMENT ME!

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

Parameters:

vox - 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(FileInfoSPM fInfo)
```
Propogates the current file info to another FileInfoSPM 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 - DOCUMENT ME!

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

Returns:

String new substring

See Also:

String.substring(int, int)

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

Parameters:

or - DOCUMENT ME!

Returns:

String the orientation string

Class FileInfoSPM

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_BYTE

DT_UNSIGNED_CHAR

DT_SIGNED_SHORT

DT_UNSIGNED_SHORT

DT_SIGNED_INT

DT_UNSIGNED_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

generated

glmax

glmin

hist_un0

hkey_un0

omax

omin

orient

origin

patient_id

regular

scale

scannum

session_error

sizeof_hdr

smax

smin

start_field

verified

views

vols_added

vox_offset

vox_units

Constructor Detail

FileInfoSPM

Method Detail

displayAboutInfo

getAuxFile

getBitPix

getCalMax

getCalMin

getCalUnits