com.openinventor.volumeviz.readers

Class SoVRSegyFileReader

java.lang.Object

com.openinventor.inventor.Inventor

com.openinventor.inventor.misc.SoBase

com.openinventor.inventor.fields.SoFieldContainer

com.openinventor.ldm.readers.SoVolumeReader

com.openinventor.volumeviz.readers.SoVRSegyFileReader

All Implemented Interfaces:

SafeDisposable

public class SoVRSegyFileReader
extends SoVolumeReader

SEGY file format reader. Reader for SEGY files (SEG Y revision 1). The following data types are supported: unsigned or signed byte, short, int32, and float.

SEGY is a widely used format for storing seismic trace data, defined by the Society of Exploration Geophysicists publication "Digital Tape Standards" (http://www.seg.org). The VolumeViz reader supports all sizes of integer and float data, and can correctly determine the number of samples per trace in most cases.

The data will be mapped to the Open Inventor axes as follows:

• The trace length is mapped onto the Inventor X axis (time).
• The number of trace sensors per line is mapped onto the Inventor Y axis (inlines).
• Z is the number of lines (crosslines).

Although in most cases the SEGY reader can automatically detect if the number of traces per line in a SEGY file is not uniform, in some cases it cannot. You can set environment variable IVVR_IRREGULAR_TRACE_NUM to request the use of a more sophisticated file parsing algorithm. However, be aware that the initialization for file reading will take longer when this environment variable is set. Missing data is assigned the value zero.

Although in most cases the SEGY reader can automatically detect if the length of traces in a SEGY data file is not uniform, in some cases it cannot. You can set environment variable IVVR_INCONSTANT_TRACE_LENGTH to request the use of a more sophisticated file parsing algorithm. However, be aware that the initialization for file reading will take significantly longer when this environment variable is set. Missing data is assigned the value zero.

In most cases the SEGY reader can automatically detect if the values in the file need to be "byte swapped", for example if the data was written on a "big-endian" machine (e.g., SPARC) and is being read on a "little-endian" machine (e.g., Intel). If necessary you can force byte swapping on or off using the environment variable IVVR_SEGY_SWAPBYTES.

A value of 1 in the format field of the SEGY header normally means that the data values were written in IBM floating point format. But in some cases the values were actually written in IEEE floating point format (which should be indicated by format = 5). Normally the SEGY reader is able to detect this, but if necessary you can specify that float values are in IEEE format by setting environment variable IVVR_SEGY_FLOATISIEEE.

If the SEGY reader fails to read the file correctly, you can set the following environment variables:

• IVVR_SEGY_DEBUG=1 This outputs information of what the reader is actually doing.
• IVVR_SEGY_DUMP=filename This requests that some information of the file and trace headers be written to the specified file while processing the SEGY data file. All these information can be sent to the VSG support for assitance.

Limitations: In some circontances few first traces might be skipped, typically when the first line contains only one trace (this trace might be skipped). In such a case a message warns the application of how many traces are actually skipped (throught SoDebugError).

See SoPreferences for information on using environment variables.

In some cases information such as line numbers and crossline numbers will be stored in non-standard locations in the header. Applications can specify the byte position of values within the header using the setSegyTraceHeaderBytePosition() method.

Information about the range of inline / crossline numbers and the range of time values can be queried using the getInlineRange(), getCrosslineRange() and getZRange() methods.

Applications can use this class to open a SEGY file and extract information from the file directly (in other words without necessarily creating a volume data node). To get the SEGY text file header call getSegyTextHeader(). To get the SEGY binary file header call getSegyFileHeader(). To get the header of a specific trace call getSegyTraceHeader(). To get the values in a specific trace call getSegyTraceData().

See also:

SoVRSegyFileHeader, SoVRSegyTraceIdHeader, SoVRSegyTraceHeaderBytePosition

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SoVRSegyFileReader.SegyAxisOrders SegY axis order mode.
static class	SoVRSegyFileReader.SegyByteOrders Segy byte order mode.
static class	SoVRSegyFileReader.SegyScanningResps SoSegyScanningCB return code.

Nested classes/interfaces inherited from class com.openinventor.ldm.readers.SoVolumeReader

SoVolumeReader.Axis, SoVolumeReader.CoordinateTypes, SoVolumeReader.CopyPolicies, SoVolumeReader.DataInfo, SoVolumeReader.ReadErrors, SoVolumeReader.ReaderTypes, SoVolumeReader.SubVolumeInfo

Nested classes/interfaces inherited from class com.openinventor.inventor.Inventor

Inventor.ConstructorCommand

Field Summary

Fields

Modifier and Type	Field and Description
static int	SCAN_ABORT Deprecated. Use SoVRSegyFileReader.SegyScanningResps.SCAN_ABORT instead.
static int	SCAN_CONTINUE Deprecated. Use SoVRSegyFileReader.SegyScanningResps.SCAN_CONTINUE instead.
static int	SEGY_BIG_ENDIAN Deprecated. Use SoVRSegyFileReader.SegyByteOrders.SEGY_BIG_ENDIAN instead.
static int	SEGY_LITTLE_ENDIAN Deprecated. Use SoVRSegyFileReader.SegyByteOrders.SEGY_LITTLE_ENDIAN instead.
static int	XYZ_AS_INLINE_CROSSLINE_SAMPLE Deprecated. Use SoVRSegyFileReader.SegyAxisOrders.XYZ_AS_INLINE_CROSSLINE_SAMPLE instead.
static int	XYZ_AS_SAMPLE_INLINE_CROSSLINE Deprecated. Use SoVRSegyFileReader.SegyAxisOrders.XYZ_AS_SAMPLE_INLINE_CROSSLINE instead.

Fields inherited from class com.openinventor.ldm.readers.SoVolumeReader

AM, AVS, COORDINATES_RECTILINEAR, COORDINATES_UNIFORM, COPY, DICOM, GENERIC, LDM, MEMORY, NO_COPY, NO_READER, RASTERSTACK, RD_FILE_FORMAT_NOT_VALID_ERROR, RD_FILE_NOT_FOUND_ERROR, RD_INVALID_DATA_ERROR, RD_NO_ERROR, RD_UNKNOWN_ERROR, RD_UNSUPPORTED_DATA_TYPE_ERROR, SEGY, TIFF, VOL, VOX, X, Y, Z

Fields inherited from class com.openinventor.inventor.Inventor

VERBOSE_LEVEL, ZeroHandle

Constructor Summary

Constructors

Constructor and Description
SoVRSegyFileReader() Constructor.

Method Summary

Modifier and Type	Method and Description
int[]	getCrosslineRange() Gets the crossline range.
int[]	getInlineRange() Gets the inline range.
int	getNumTraces() Returns the number of traces.
SbVec2d[]	getP1P2P3Coordinates() Gets the P1, P2, P3 and P4 coordinates.
SoVRSegyFileReader.SegyAxisOrders	getSegyAxisOrder() Get the storage order for X, Y, and Z axis.
SoVRSegyFileReader.SegyByteOrders	getSegyByteOrder() Gets the byte ordering to use when reading the SEGY file.
SoVRSegyFileHeader	getSegyFileHeader() Calls getSegyFileHeader((boolean)false).
SoVRSegyFileHeader	getSegyFileHeader(boolean readFile) Gets the SEGY file header.
java.lang.String	getSegyTextHeader() Retreives the textual header (the first 3200-bytes) of the SEGY file.
SoVRSegyTraceIdHeader	getSegyTraceHeader(int traceNumber) Gets the SEGY trace header of the given trace traceNumber .
SoVRSegyTraceHeaderBytePosition	getSegyTraceHeaderBytePosition() Gets the byte positions within the trace header.
SbVec2d	getTraceCoord(int i, int j)
int[]	getZRange() Gets the Z (time axis range.
boolean	isSegyRegular() Sets the trace header of a specific trace used to read the SEGY file [OPTIONAL].
void	setCrosslineRange(int from, int to, int step) Sets the crossline range.
void	setInlineRange(int from, int to, int step) Sets the inline range.
void	setSegyAxisOrder(SoVRSegyFileReader.SegyAxisOrders axisOrder) Sets the storage order for X, Y, and Z axes.
void	setSegyByteOrder(SoVRSegyFileReader.SegyByteOrders byteOrder) Sets the byte ordering to use when reading the SEGY file.
boolean	setSegyFileHeader(SoVRSegyFileHeader fileHeader) Specifies the header used to read the SEGY file.
void	setSegyTextHeaderAscii(boolean ascii) Tells whether the textual header format is ASCII or not.
void	setSegyTraceHeaderBytePosition(SoVRSegyTraceHeaderBytePosition traceHeaderBytePosition) Tells the file reader where the fields are actually located (i.e., the byte positions) within the trace header.
static void	setVolumeSizeVoxels(boolean flag) If true, the volume extent (bounds in world coordinates) is set to 0 to dimension-1 on each axis.
void	setZRange(int from, int to, int step) Sets the Z (time axis) range.

Methods inherited from class com.openinventor.ldm.readers.SoVolumeReader

closeAllHandles, getAppropriateReader, getBorderFlag, getConfiguredWriter, getCoordinateType, getCurrentTimeStep, getDataChar, getDirectCoordSys, getDirectCoordSysAutoDetection, getDoubleMinMax, getFilename, getIntMinMax, getMinMax, getNumSignificantBits, getNumSubsampledTiles, getNumTimeSteps, getNumVoxels, getOriginalFilename, getReaderType, getShortTileSize, getSizeToAllocate, getSubSlice, getSubVolumeInfo, getTileMinMax, getTileSize, isDataConverted, isIgnoredFile, isRGBA, isThreadSafe, readTile, readTile, restoreAllHandles, setCurrentTimeStep, setDirectCoordSysAutoDetection, setDirectCoorSys, setFilename, setInputDataRange, setOutputDataType, setRectilinearCoordinates, setRGBA

Methods inherited from class com.openinventor.inventor.fields.SoFieldContainer

copyFieldValues, copyFieldValues, enableNotify, fieldsAreEqual, get, getAllFields, getEventIn, getEventOut, getField, getFieldName, hasDefaultValues, isNotifyEnabled, set, setToDefaults

Methods inherited from class com.openinventor.inventor.misc.SoBase

dispose, getEXTERNPROTO, getName, getPROTO, isDisposable, isSynchronizable, setName, setSynchronizable, touch

Methods inherited from class com.openinventor.inventor.Inventor

getAddress, getNativeResourceHandle, startInternalThreads, stopInternalThreads

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SCAN_CONTINUE

@Deprecated
public static final int SCAN_CONTINUE

Deprecated. Use SoVRSegyFileReader.SegyScanningResps.SCAN_CONTINUE instead.

SCAN_ABORT

@Deprecated
public static final int SCAN_ABORT

Deprecated. Use SoVRSegyFileReader.SegyScanningResps.SCAN_ABORT instead.

SEGY_LITTLE_ENDIAN

@Deprecated
public static final int SEGY_LITTLE_ENDIAN

Deprecated. Use SoVRSegyFileReader.SegyByteOrders.SEGY_LITTLE_ENDIAN instead.

SEGY_BIG_ENDIAN

@Deprecated
public static final int SEGY_BIG_ENDIAN

Deprecated. Use SoVRSegyFileReader.SegyByteOrders.SEGY_BIG_ENDIAN instead.

XYZ_AS_SAMPLE_INLINE_CROSSLINE

@Deprecated
public static final int XYZ_AS_SAMPLE_INLINE_CROSSLINE

Deprecated. Use SoVRSegyFileReader.SegyAxisOrders.XYZ_AS_SAMPLE_INLINE_CROSSLINE instead.

XYZ_AS_INLINE_CROSSLINE_SAMPLE

@Deprecated
public static final int XYZ_AS_INLINE_CROSSLINE_SAMPLE

Deprecated. Use SoVRSegyFileReader.SegyAxisOrders.XYZ_AS_INLINE_CROSSLINE_SAMPLE instead.

Constructor Detail

SoVRSegyFileReader

public SoVRSegyFileReader()

Constructor.

Method Detail

getSegyFileHeader

public SoVRSegyFileHeader getSegyFileHeader()

Calls getSegyFileHeader((boolean)false).

getSegyTextHeader

public java.lang.String getSegyTextHeader()

Retreives the textual header (the first 3200-bytes) of the SEGY file.

getSegyByteOrder

public SoVRSegyFileReader.SegyByteOrders getSegyByteOrder()

Gets the byte ordering to use when reading the SEGY file.

setSegyByteOrder

public void setSegyByteOrder(SoVRSegyFileReader.SegyByteOrders byteOrder)

Sets the byte ordering to use when reading the SEGY file. The default value is SEGY_LITTLE_ENDIAN. In most cases, even when the SEGY file is big endian, the SEGY file reader is able to detect this and read the file accordingly. This method is for the very rare case when the automatic byte order detection fails.

setSegyFileHeader

public boolean setSegyFileHeader(SoVRSegyFileHeader fileHeader)

Specifies the header used to read the SEGY file. If this method is called, the reader uses the binary file header you pass rather than the actual binary file header. The following fields from the binary file header are used:

• formatRevisionNumber
• numTextHeaderExt
• format
• fixedLengthTraceFlag
• hns (number of samples per trace)

Returns false if the operation fails, for example, if SoVolumeReader.setFilename() was not called first.

setVolumeSizeVoxels

public static void setVolumeSizeVoxels(boolean flag)

If true, the volume extent (bounds in world coordinates) is set to 0 to dimension-1 on each axis. Else the volume extent is normalized to fit inside a unit cube centered at the origin. In other words, the size will be -.5 to +.5 along the longest dimension. false by default. The application can also set the volume extent to whatever is appropriate by setting the SoVolumeData node's extent field.

setSegyTextHeaderAscii

public void setSegyTextHeaderAscii(boolean ascii)

Tells whether the textual header format is ASCII or not. The default value is false, i.e., the textual header format is EBCDIC

setZRange

public void setZRange(int from,
                      int to,
                      int step)

Sets the Z (time axis) range. Note that this setting does not limit the amount of data read from the file (although a subclass could do that). It just specifies the range values that will be returned by getZRange().

getCrosslineRange

public int[] getCrosslineRange()

Gets the crossline range. This method returns the actual values from the file if the corresponding set method has not been called previously. Otherwise, the values previously specified with setCrosslineRange are returned.

getSegyAxisOrder

public SoVRSegyFileReader.SegyAxisOrders getSegyAxisOrder()

Get the storage order for X, Y, and Z axis. See setSegyAxisOrder().

setInlineRange

public void setInlineRange(int from,
                           int to,
                           int step)

Sets the inline range. Note that this setting does not limit the amount of data read from the file (although a subclass could do that). It just specifies the range values that will be returned by getInlineRange().

setSegyAxisOrder

public void setSegyAxisOrder(SoVRSegyFileReader.SegyAxisOrders axisOrder)

Sets the storage order for X, Y, and Z axes.
For example, XYZ_AS_INLINE_CROSSLINE_SAMPLE means lines along X, crosslines along Y, and samples along Z axis.

The default value is XYZ_AS_SAMPLE_INLINE_CROSSLINE, meaning samples along X, lines along Y, and crosslines along Z axis.

Note: You must call this method before:

• Calling getDataChar()
• Calling setFilename(), or
• Setting the reader in an SoVolumeData node.

(Because the last two operations indirectly cause getDataChar() to be called.)

getP1P2P3Coordinates

public SbVec2d[] getP1P2P3Coordinates()

Gets the P1, P2, P3 and P4 coordinates. P1, P2 are on the corners corresponding to the first line. P4, P3 are on the corners corresponding to the last line. If these points do not exist, the crossline and inline values are used instead. Returns true for a right-handed coordinate system (Xline/Inline/Time).

getZRange

public int[] getZRange()

Gets the Z (time axis range. This method returns the actual values from the file if the corresponding set method has not been called previously. Otherwise, the values previously specified with setZRange are returned.

getInlineRange

public int[] getInlineRange()

Gets the inline range. This method returns the actual values from the file if the corresponding set method has not been called previously. Otherwise, the values previously specified with setInlineRange are returned.

NOTE: If the inline values are incorrect in the file, or are not retrieved correctly for any reason, getInlineRange returns (1, numLines, 1).

getTraceCoord

public SbVec2d getTraceCoord(int i,
                             int j)

getSegyTraceHeaderBytePosition

public SoVRSegyTraceHeaderBytePosition getSegyTraceHeaderBytePosition()

Gets the byte positions within the trace header.

setSegyTraceHeaderBytePosition

public void setSegyTraceHeaderBytePosition(SoVRSegyTraceHeaderBytePosition traceHeaderBytePosition)

Tells the file reader where the fields are actually located (i.e., the byte positions) within the trace header. Only the field SEGY_CDP is used (Xline position).

getSegyFileHeader

public SoVRSegyFileHeader getSegyFileHeader(boolean readFile)

Gets the SEGY file header. If you use this class to read a SEGY file directly, you will have to call the method SoVolumeReader.setFilename() first. Returns false if the operation fails, for example, if SoVolumeReader.setFilename() was not called first. If readFile is true the file header is read from the file, otherwise the value set by setSegyFileHeader() is returned instead. If readFile is false but setSegyFileHeader() was never called, the file header is read from the file anyway.

getNumTraces

public int getNumTraces()

Returns the number of traces. If the file is not regular (see isSegyRegular()), an approximate number (considering it as regular) is returned (to avoid scanning the whole file).

setCrosslineRange

public void setCrosslineRange(int from,
                              int to,
                              int step)

Sets the crossline range. Note that this setting does not limit the amount of data read from the file (although a subclass could do that). It just specifies the range values that will be returned by getCrosslineRange().

isSegyRegular

public boolean isSegyRegular()

Sets the trace header of a specific trace used to read the SEGY file [OPTIONAL]. Indicates if SEGY file is regular. A file with the same number of traces in each inline and with the same number of samples for each trace is considered as regular.

getSegyTraceHeader

public SoVRSegyTraceIdHeader getSegyTraceHeader(int traceNumber)

Gets the SEGY trace header of the given trace traceNumber . traceNumber can range from zero to the number of traces minus one. If you use this class to read a SEGY file directly, you will have to call the method SoVolumeReader.setFilename() first. Returns false if the operation fails, for example, if SoVolumeReader.setFilename() was not called first.