Types data structures and functions for reading and writing external file formats to and from Woolz objects. See the libWlzExt for more detail. All procedures are detailed under different module headings. More...

Files
file	WlzExtFF.c
	Functions for reading and writting Woolz objects to and from external data formats.

file	WlzExtFF.h
	Main header file for external data file format support for the MRC Human Genetics Unit Woolz library.

file	WlzExtFFAm.c
	Functions for reading and writting Woolz objects to the Amira lattice file format.

file	WlzExtFFAnl.c
	Functions for reading and writting Woolz objects to the ANALYZE 7.5 format file.

file	WlzExtFFBibUtils.c
	Woolz IO bibfile utility functions to write and parse records written in bibfile format.

file	WlzExtFFBmp.c
	Functions for reading and writting Woolz objects to and from the portable anymap '.pnm' data format.

file	WlzExtFFDen.c
	Functions for reading and writting Woolz objects to and from the Stanford University '.den' data format.

file	WlzExtFFEMT.c
	Functions for reading and writting Woolz objects to and from the the Netgen neutral (tetrahedral) mesh file format.

file	WlzExtFFGif.c
	Functions for reading Woolz objects from Graphics Interchange Format (GIF) images.

file	WlzExtFFIcs.c
	Functions for reading and writting Woolz objects to and from the International Cytometry Standard '.ics'/'.ids' data format.

file	WlzExtFFIPL.c
	Functions for reading and writing IPLab image formats.

file	WlzExtFFJpeg.c
	Read and write procedures for Joint Expert Group image format JPEG.

file	WlzExtFFMesh.c
	Functions for reading and writting Woolz objects to and from the the tetrahedral mesh file format used by Pascal Frey's medit. See the INRIA technical report 0253 for a detailed explaination of the fromat. This file format is also used by the tetrhedral mesh generator tetgen.

file	WlzExtFFNifti.c
	Functions for reading and writting Woolz objects to the NIfTI format.

file	WlzExtFFNodeEle.c
	Functions for reading and writting Woolz objects to and from the the two part .node/.ele tetrahedral mesh file format used by Jonathan Shewchuk in Stellar.

file	WlzExtFFNrrd.c
	Functions for reading and writting Woolz objects to and from the Utah nearly raw raster data (NRRD) '.nrrd' single file data format.

file	WlzExtFFObj.c
	Functions for reading and writting Woolz objects to and from the the OBJ Wavefront geometry file format.

file	WlzExtFFPic.c
	Functions for reading and writting Woolz objects to and from the Biorad '.pic' data format.

file	WlzExtFFPly2.c
	Functions for reading and writting Woolz objects to and from the the Riken PLY2 file format.

file	WlzExtFFPnm.c
	Functions for reading and writting Woolz objects to and from the portable anymap '.pnm' data format.

file	WlzExtFFPvl.c
	Functions for reading and writting Woolz objects to the Drishti pvl.nc file format.

file	WlzExtFFRaw.c
	Read/write raw image data.

file	WlzExtFFSlc.c
	Functions for reading and writting Woolz objects to and from the '.slc' data format.

file	WlzExtFFSMesh.c
	Functions for reading and writting Woolz objects to and from the the GRUMMP surface mesh (smesh) file format.

file	WlzExtFFStack.c
	Functions for reading and writting Woolz objects to and from a stack of 2D files.

file	WlzExtFFStl.c
	Functions for reading and writting Woolz objects to and from the the stereolithography stl surface file sormat.

file	WlzExtFFTiff.c
	I/O functions for tiff format images.

file	WlzExtFFTxt.c
	Functions for writing Woolz objects to a simple text '.txt' data format.

file	WlzExtFFType.h
	Header file with data types for external data file format support for the MRC Human Genetics Unit Woolz library.

file	WlzExtFFVff.c
	Functions for reading and writting Woolz objects to and from the Sunvision '.vff' data format.

file	WlzExtFFVMesh.c
	Functions for reading and writting Woolz objects to and from the the GRUMMP VMESH tetrahedral mesh file format.

file	WlzExtFFVtk.c
	Functions for reading and writting Woolz objects to and from the VTK '.vtk' data format.

Data Structures
struct	_WlzEffAmMaterial
	Item in an Amira material list. Typedef: WlzEffAmMaterial. More...

struct	_WlzEffAmHead
	Head of a list of Amira materials. Typedef: WlzEffAmHead. More...

struct	_WlzEffAnlComplex
	Analyze 7.5 complex number representation. Typedef: WlzEffAnlComplex. More...

struct	_WlzEffAnlHeaderKey
	Analyze 7.5 file header key. Typedef: WlzEffAnlFileKey. More...

struct	_WlzEffAnlImageDim
	Analyze 7.5 file header structure for the image dimensions. Typedef: WlzEffAnlImageDim. More...

struct	_WlzEffAnlDataHistory
	Analyze 7.5 file header structure for the image history. Typedef: WlzEffAnlDataHistory. More...

struct	_WlzEffAnlDsr
	Analyze 7.5 file header. Typedef: WlzEffAnlDsr. More...

Enumerations
enum	_WlzEffFormat { WLZEFF_FORMAT_NONE = 0, WLZEFF_FORMAT_BMP, WLZEFF_FORMAT_DEN, WLZEFF_FORMAT_ICS, WLZEFF_FORMAT_PNM, WLZEFF_FORMAT_PIC, WLZEFF_FORMAT_SLC, WLZEFF_FORMAT_VFF, WLZEFF_FORMAT_VTK, WLZEFF_FORMAT_WLZ, WLZEFF_FORMAT_IPL, WLZEFF_FORMAT_TIFF, WLZEFF_FORMAT_RAW, WLZEFF_FORMAT_AM, WLZEFF_FORMAT_JPEG, WLZEFF_FORMAT_ANL, WLZEFF_FORMAT_GIF, WLZEFF_FORMAT_MESH, WLZEFF_FORMAT_NODEELE, WLZEFF_FORMAT_VMESH, WLZEFF_FORMAT_PLY2, WLZEFF_FORMAT_OBJ, WLZEFF_FORMAT_TXT, WLZEFF_FORMAT_NIFTI, WLZEFF_FORMAT_SMESH, WLZEFF_FORMAT_EMT, WLZEFF_FORMAT_STL, WLZEFF_FORMAT_PVL, WLZEFF_FORMAT_NRRD, WLZEFF_FORMAT_COUNT }
	enumeration of the file formats supported. Typedef: WlzEffFormat More...

enum	_WlzEffAmToken { WLZEFF_AM_TOKEN_NONE = (0), WLZEFF_AM_TOKEN_BOUNDINGBOX, WLZEFF_AM_TOKEN_CLOSE, WLZEFF_AM_TOKEN_COLOR, WLZEFF_AM_TOKEN_COLORMAP, WLZEFF_AM_TOKEN_CONTENT, WLZEFF_AM_TOKEN_COORDTYPE, WLZEFF_AM_TOKEN_DEFINE, WLZEFF_AM_TOKEN_EXPRESSION, WLZEFF_AM_TOKEN_HASH, WLZEFF_AM_TOKEN_ID, WLZEFF_AM_TOKEN_IMAGEDATA, WLZEFF_AM_TOKEN_LATTICE, WLZEFF_AM_TOKEN_MATERIALS, WLZEFF_AM_TOKEN_NAME, WLZEFF_AM_TOKEN_OPEN, WLZEFF_AM_TOKEN_PARAMETERS, WLZEFF_AM_TOKEN_SEEDS, WLZEFF_AM_TOKEN_LIMITS, WLZEFF_AM_TOKEN_TIFF, WLZEFF_AM_TOKEN_TRANSFORM }
	Tokens for parsing the headers of Amira lattice files. Typedef: WlzEffAmToken. More...

enum	_WlzEffAmDim { WLZEFF_AM_DIM_NONE = (0), WLZEFF_AM_DIM_2 = (2), WLZEFF_AM_DIM_3 = (3) }
	Dimension of the data. Typedef: WlzEffAmDim. More...

enum	_WlzEffAmEndian { WLZEFF_AM_ENDIAN_NONE = (0), WLZEFF_AM_ENDIAN_BIG = (10), WLZEFF_AM_ENDIAN_LITTLE = (11) }
	Big or little endian binary data. The values endian enum must be kept distinct from the dimension enum values (apart from none). Typedef: WlzEffAmFormat. More...

enum	_WlzEffAmFormat { WLZEFF_AM_FMT_NONE = (0), WLZEFF_AM_FMT_BINARY = (1), WLZEFF_AM_FMT_ASCII = (2) }
	ASCII or binary data. Typedef: WlzEffAmFormat. More...

enum	_WlzEffAmDatType { WLZEFF_AM_DATTYPE_NONE = (0), WLZEFF_AM_DATTYPE_BYTE = (1), WLZEFF_AM_DATTYPE_SHORT = (2) }
	Type of data: byte, ... Typedef: WlzEffAmDatType. More...

enum	_WlzEffAmCoordType { WLZEFF_AM_COORDTYPE_NONE = (0), WLZEFF_AM_COORDTYPE_UNITFORM = (1) }
	Type of coordinate system. Typedef: WlzEffAmCoordType. More...

enum	_WlzEffAmLatComp { WLZEFF_AM_LATCOMP_NONE = (0), WLZEFF_AM_LATCOMP_HXBYTERLE = (1) }
	Type of compression used. Typedef: WlzEffAmLatComp. More...

enum	_WlzEffAmLatType { WLZEFF_AM_LATTYPE_NONE = (0), WLZEFF_AM_LATTYPE_DATA = (1), WLZEFF_AM_LATTYPE_LABELS = (2) }
	Type of lattice: uniform, ... Typedef: WlzEffAmLatType. More...

enum	_WlzEffAnlDataType { WLZEFF_ANL_DT_NONE = 0, WLZEFF_ANL_DT_UNKOWN = 0, WLZEFF_ANL_DT_BINARY = 1, WLZEFF_ANL_DT_UNSIGNED_CHAR = 2, WLZEFF_ANL_DT_SIGNED_SHORT = 4, WLZEFF_ANL_DT_SIGNED_INT = 8, WLZEFF_ANL_DT_FLOAT = 16, WLZEFF_ANL_DT_COMPLEX = 32, WLZEFF_ANL_DT_DOUBLE = 64, WLZEFF_ANL_DT_RGB = 128, WLZEFF_ANL_DT_ALL = 255 }
	Valid Analyze data type values. Typedef: WlzEffAnlDataType. More...

Functions
WlzEffFormat	WlzEffStringExtToFormat (const char *extStr)
	Returns a file format for the given file extension string. More...

WlzEffFormat	WlzEffStringToFormat (const char *fmtStr)
	Returns a file format for the given file format string. More...

const char *	WlzEffStringFromFormat (WlzEffFormat fileFmt, const char **dstExtStr)
	Returns a string which is suitable for displaying the given format and sets a destination pointer for the formats file extension. More...

WlzEffFormat	WlzEffStringFormatFromFileName (const char *fNameStr)
	Returns a the file format implied by the file extension used in the given file name. If no match is found WlzEffFormat::WLZEFF_FORMAT_NONE is returned. More...

WlzObject *	WlzEffReadObj (FILE fP, const char fName, WlzEffFormat fFmt, int split, int sTrans, int gTrans, WlzErrorNum *dstErr)
	Reads a woolz object from the the given file names(s) or opened file, where the file format is that given as a parameter. The ANL, ICS, PNM (and a few other multi file formats) require a file name, for all other formats either the file name or a file pointer may be given. More...

WlzErrorNum	WlzEffWriteObj (FILE fP, const char fName, WlzObject *obj, WlzEffFormat fFmt)
	Writes a woolz object to the the given file stream, with the given file format. More...

int	WlzEffNumberOfFormats (void)
	Retuns the number of file formats, ie WLZEFF_FORMAT_COUNT - 1. More...

char *	WlzEffFormatTable (unsigned indWth, unsigned desWth, unsigned extWth, WlzErrorNum *dstErr)
	Creates an ascii table of the valid formats supported by WlzExtFF. This may be useful for giving usage information in binaries. More...

WlzObject *	WlzEffReadObjAm (FILE fP, int split, WlzErrorNum dstErr)
	Reads a Woolz object from the given file using the Amira lattice (.am file) format. More...

WlzErrorNum	WlzEffWriteObjAm (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given file using the Amira lattice (.am file) format. More...

WlzErrorNum	WlzEffAnlFileNames (char fileBody, char hdrFileName, char *imgFileName, const char gvnFileName)
	Builds the ANALYZE file names from the given file name. These strings should be free'd using AlcFree() when no longer required. More...

WlzObject *	WlzEffReadObjAnl (const char gvnFileName, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the ANALYZE 7.5 format. The given file name is used to generate the '.hdr' and '.img' filenames. More...

WlzErrorNum	WlzEffWriteObjAnl (const char gvnFileName, WlzObject obj)
	Writes the given Woolz object to the given file(s) using the ANALYZE 7.5 file format. The given file name is used to generate the '.hdr' and '.img' filenames. More...

WlzThreeDViewStruct *	WlzEffBibRead3DView (FILE fP, char dstMsg, WlzErrorNum dstErr)
	Reads a 3D view from the given file pointer. More...

WlzErrorNum	WlzEffBibWrite3DSectionViewParamsRecord (FILE fp, char recordName, WlzThreeDViewStruct *wlzViewStr)
	Write the section view parameters in the bibtex style record using the bibFile library. More...

WlzErrorNum	WlzEffBibParse3DSectionViewParamsRecord (BibFileRecord bibfileRecord, WlzThreeDViewStruct wlzViewStr)
	Parse the bibfile record for a woolz 3D view structure setting paramters in the given view structure. More...

WlzErrorNum	WlzEffBibWriteWarpTransformParamsRecord (FILE fp, char recordName, WlzFnType basisFnType, WlzTransformType affineType, WlzMeshGenMethod meshMthd, int meshMinDst, int meshMaxDst)
	Write the details of a warp transformation parameters. Note this does not write the warp transformation itself. More...

WlzErrorNum	WlzEffBibParseWarpTransformParamsRecord (BibFileRecord bibfileRecord, WlzFnType basisFnType, WlzTransformType affineType, WlzMeshGenMethod meshMthd, int meshMinDst, int meshMaxDst)
	Parse the bibfile record for the warp transformation parameter settings. More...

WlzErrorNum	WlzEffBibWriteTiePointVtxsRecord (FILE fp, char recordName, int index, WlzDVertex3 dstVtx, WlzDVertex3 srcVtx, int relativeFlg)
	Write a tie-point record in bibtex style. More...

WlzErrorNum	WlzEffBibParseTiePointVtxsRecord (BibFileRecord bibfileRecord, int index, WlzDVertex3 dstVtx, WlzDVertex3 srcVtx, int *relativeFlg)
	Parse the bibfile record for a tie-point pair of vertices. The record should also include an index so that tie-point ordering is preserved. More...

WlzErrorNum	WlzEffBibWriteFileRecord (FILE fp, char recordName, char *fileName, WlzEffFormat fileType)
	Write a bibfile record to record the file name and file type. More...

WlzErrorNum	WlzEffBibParseFileRecord (BibFileRecord bibfileRecord, int dstIndex, char *dstFileName, WlzEffFormat dstFileType)
	Parse a bibfile record for a filename and type. More...

WlzErrorNum	WlzEffBibWriteWarpInputSegmentationParamsRecord (FILE fp, char recordName, int normFlg, int histoFlg, int shadeFlg, int gaussFlg, double width)
	Write a warp segmentation parameter record i.e. the image processing operations and paramters for extracting the gene-expression domain. More...

WlzErrorNum	WlzEffBibParseWarpInputSegmentationParamsRecord (BibFileRecord bibfileRecord, int normFlg, int histoFlg, int shadeFlg, int gaussFlg, double width, int threshLow, int threshHigh)
	Parse the bibfile record for a MAPaint WarpInputSegmentationParams record. More...

WlzObject *	WlzEffReadObjBmp (const char gvnFileName, WlzErrorNum dstErr)
	Reads a Woolz object from the given file(s) using the '.pnm' file format. More...

WlzErrorNum	WlzEffWriteObjBmp (const char gvnFileName, WlzObject obj)
	Writes the given Woolz object to the given file(s) using the '.pnm' file format. More...

WlzErrorNum	WlzEffWriteObjBmp2D (const char fNameStr, WlzObject obj, WlzIVertex2 imgSz, WlzIVertex2 imgOrg, unsigned char *data, unsigned char bgd)
	Writes the given 2D Woolz object to the given file using the '.pnm' file format. More...

WlzErrorNum	WlzEffReadObjBmpData2D (FILE fP, WlzIVertex2 gvnImgSz, unsigned char ***data)
	Reads the data from a pgm file into the data array given. More...

WlzObject *	WlzEffReadObjDen (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the Stanford density file format. More...

WlzErrorNum	WlzEffWriteObjDen (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the Stanford density file format. More...

WlzObject *	WlzEffReadObjEMT (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the GRUMMP vmesh tetrahedral mesh file format. More...

WlzErrorNum	WlzEffWriteObjEMT (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the Netgen neutral mesh file format. More...

WlzObject *	WlzEffReadObjGif (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the file pointer using the '.gif' file format. This function currently has the following limitations: More...

WlzErrorNum	WlzEffIcsFileNames (char fileBody, char icsFileName, char *idsFileName, const char gvnFileName)
	Builds the ics file names from the given file name. These strings should be free'd using AlcFree() when no longer required. More...

WlzObject *	WlzEffReadObjIcs (const char gvnFileName, WlzErrorNum dstErr)
	Reads a Woolz object from a pair of files using the ICS format. The given file name is used to generate the '.ics' and '.ids' filenames. More...

WlzErrorNum	WlzEffWriteObjIcs (const char gvnFileName, WlzObject obj)
	Writes the given Woolz object to a pair of files using the ICS format. The given file name is used to generate the '.ics' and '.ids' filenames. More...

WlzObject *	WlzEffReadObjIPL (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the '.ipl' file format. More...

WlzErrorNum	WlzEffWriteObjIPL (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the '.ipl' file format. More...

static WlzErrorNum	WlzEffHeadWriteIPL (WlzEffIPLHeader header, FILE fP)
	Writes an IPL header to the given file stream. More...

WlzObject *	WlzEffReadObjJpeg (FILE fP, WlzErrorNum dstErr)
	Reads a jpeg image frm the given file stream and returns a Woolz object. More...

WlzErrorNum	WlzEffWriteObjJpeg (FILE fP, WlzObject obj, char *params)
	Writes the given object to a jpeg image. More...

WlzObject *	WlzEffReadObjMesh (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using Pascal Frey's tetrahedral mesh file format. The file must start with the records: More...

WlzErrorNum	WlzEffWriteObjMesh (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using Pascal Frey's tetrahedral mesh file format. See WlzEffReadObjMesh() for details of the format. More...

WlzObject *	WlzEffReadObjNifti (const char gvnFileName, int sTrans, int gTrans, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the NIfTI format. In some cases (for example when the NIfTI object has complex values) a compound object may be returned. A text property is created for the returned object, containing various fields of the NIfTI header, some of which may not be used in the conversion. The qform transform/quaternion, mapping the image to it's source (scanner) coordinates is copied text property but no transform is either created of applied for it. The sform transform/quaternion is always applied if the parameter flag is set, otherwise it ionly is applied if it is a pure translation. If the sform transform is not applied then it will (if not an identity transform) be used to create a trans-obj. If affine transforms are applied then WLZ_INTERPOLATION_NEAREST is used. NIfTI allows the linear transformation of grey values. This will only be applied if the parameter flag is set. The grey scaling will result in floating point image grey values. More...

WlzErrorNum	WlzEffWriteObjNifti (const char gvnFileName, WlzObject obj)
	Writes the given Woolz object to the given file(s) using the NIfTI file format. More...

WlzErrorNum	WlzEffNodeEleFileNames (char fileBody, char nodeFileName, char *eleFileName, const char gvnFileName)
	Builds the node/ele file names from the given file name. These strings should be free'd using AlcFree() when no longer required. More...

WlzObject *	WlzEffReadObjNodeEle (const char gvnFileName, WlzErrorNum dstErr)
	Reads a Woolz object from a pair of files using the node/ele format. The given file name is used to generate the '.node' and '.ele' filenames. More...

WlzErrorNum	WlzEffWriteObjNodeEle (const char gvnFileName, WlzObject obj)
	Writes the given Woolz object to a pair of files using the node/ele two part mesh file format. The given file name is used to generate the '.node' and '.ele' filenames. More...

WlzObject *	WlzEffReadObjNrrd (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the NRRD file format. Not all NRRD files and not all encodings have been implemented. This function will currently only read pixel/voxel data, where this data is either raw or encoded using bzip2 or gzip compression. Use of these compression methods depends on their availability at compile time. If the input NRRD pixel/voxel type is either signed char or unsigned short then it is promoted to either signed short or signed int in the output Woolz object. Unused NRRD header fields are encoded as a text property of the output object. More...

WlzErrorNum	WlzEffWriteObjNrrd (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the NRRD file format. This function will currently only write 2 or 3D domain objects. If the object has no values then unsigned byte values are written with background = 0 and forground = 255. If gzip compression is available at compile time the output file uses gzip compression, otherwise raw data are output. More...

WlzObject *	WlzEffReadObjObj (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the Wavefront OBJ file format. This format consists of the following possible fields (one per line): Vertex data -v vertex geometry -vt ignored -vn vertex normal -vp ignored -cstype ignored -deg ignored -bmat ignored -step ignored Elements -p ignored -l ignored -f face -curv ignored -curv2 ignored -surf ignored Freeform elements -param ignored -trim ignored -hole ignored -scrv ignored -sp ignored -end ignored Freeform surface connectivity -con ignored Grouping -g ignored -o ignored -s ignored -mg ignored Rendering attributes -bevel ignored -c_interp ignored -d_interp ignored -lod ignored -usemtl ignored -mtllib ignored -shadow_obj ignored -trace_obj ignored -ctech ignored -stech ignored Comments ignored Only triangulated surface models can be read. All groupings will be amalgamated into one. More...

WlzErrorNum	WlzEffWriteObjObj (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given file stream using the Wavefront OBJ file format, see WlzEffReadObjObj(). More...

WlzObject *	WlzEffReadObjPic (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the BioRad Confocal '.pic' format. More...

WlzErrorNum	WlzEffWriteObjPic (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the BioRad Confocal '.pic' format. More...

WlzObject *	WlzEffReadObjPly2 (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the Riken PLY2 triangular mesh file format. This format simply consists of: More...

WlzErrorNum	WlzEffWriteObjPly2 (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given file stream using the Riken PLY2 triangular mesh file format, see WlzEffReadObjPly2(). More...

WlzObject *	WlzEffReadObjPnm (const char gvnFileName, WlzErrorNum dstErr)
	Reads a Woolz object from the given file(s) using the '.pnm' file format. More...

WlzErrorNum	WlzEffWriteObjPnm (const char gvnFileName, WlzObject obj)
	Writes the given Woolz object to the given file(s) using the '.pnm' file format. More...

WlzErrorNum	WlzEffWriteObjPnm2D (const char fNameStr, WlzObject obj, WlzIVertex2 imgSz, WlzIVertex2 imgOrg, unsigned char *data, unsigned char bgd)
	Writes the given 2D Woolz object to the given file using the '.pnm' file format. More...

WlzErrorNum	WlzEffReadObjPnmData2D (FILE fP, WlzIVertex2 gvnImgSz, unsigned char ***data)
	Reads the data from a pgm file into the data array given. More...

WlzObject *	WlzEffReadObjPvl (const char gvnFileName, WlzErrorNum dstErr)
	Reads a Woolz object from Drishti pvl.nc files. More...

WlzErrorNum	WlzEffWriteObjPvl (const char gvnFileName, WlzObject obj)
	Writes the given Woolz object to a pair of files using the Derishti .pvl.nc file format. More...

WlzObject *	WlzExtFFReadObjRaw (FILE fp, int numKols, int numLines, int numPlanes, int bytesPerPixel, int bitsPerChannel, int numChannels, int byteOrder, WlzErrorNum dstErr)
	Reads a raw 'brick of bytes' object into a Woolz object. More...

WlzObject *	WlzEffReadObjSlc (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the '.slc' file format. More...

WlzErrorNum	WlzEffWriteObjSlc (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the '.slc' file format. More...

WlzObject *	WlzEffReadObjSMesh (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the GRUMMP smesh file format. This format is: More...

WlzErrorNum	WlzEffWriteObjSMesh (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given file stream using the GRUMMP smesh file format, see WlzEffReadObjSMesh(). More...

WlzObject *	WlzEffReadObjStack (const char gvnFileName, WlzEffFormat fFmt, WlzErrorNum dstErr)
	Reads a Woolz object from the given file(s) using the given (2D) file format. More...

WlzErrorNum	WlzEffWriteObjStack (const char gvnFileName, WlzEffFormat fFmt, WlzObject obj)
	Writes the given Woolz object to the given file(s) using the given (2D) file format. More...

WlzObject *	WlzEffReadObjStl (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the stereolithography stl surface file format. This format has surface definitions defined by a name and a collection of facet normals and loops. Each facet loop has the cooordinates of it's vertices. Only triangulated surface models can be read and all solids will be treated as one. More...

WlzErrorNum	WlzEffWriteObjStl (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given file stream using the stereolithography stl file format, see WlzEffReadObjStl(). More...

WlzObject *	WlzEffReadObjTiff (const char tiffFileName, int split, WlzErrorNum dstErr)
	Reads a Woolz object from the given file using the TIFF format. More...

WlzErrorNum	WlzEffWriteObjTiff (const char tiffFileName, WlzObject obj)
	Writes the given Woolz object to the given file using the TIFF format. More...

WlzObject *	WlzEffReadObjVff (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the Sunvision vff (rank 3) file format. More...

WlzErrorNum	WlzEffWriteObjVff (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the Sunvision vff (rank 3) file format. More...

WlzObject *	WlzEffReadObjVMesh (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the GRUMMP vmesh tetrahedral mesh file format. More...

WlzErrorNum	WlzEffWriteObjVMesh (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the GRUMP VMESH tetrahedral mesh file format. More...

WlzObject *	WlzEffReadObjVtk (FILE fP, WlzErrorNum dstErr)
	Reads a Woolz object from the given stream using the Visualization Toolkit file format. There is no check on the major and minor version numbers since all files seem compatable. More...

WlzErrorNum	WlzEffWriteObjVtk (FILE fP, WlzObject obj)
	Writes the given Woolz object to the given stream using the Visualization Toolkit file format. More...

WlzErrorNum	WlzEffWritePointsVtk (FILE fP, WlzObject obj, int onlyDom)
	Writes the given Woolz points object to the given stream using the Visualization Toolkit polydata format, but without polygons. More...

WlzErrorNum	WlzEffWritePointsVtkScalarValues (FILE fP, WlzObject obj)
	Writes the point scalar values of the given object to the given file. It is assumed that the points domain has already been written by WlzEffWritePointsVtk(). More...

WlzErrorNum	WlzEffWritePointsVtkFieldValues (FILE fP, WlzObject obj)
	Writes the point field values of the given object to the given file. It is assumed that the points domain has already been written by WlzEffWritePointsVtk(). More...

Detailed Description

Types data structures and functions for reading and writing external file formats to and from Woolz objects. See the libWlzExt for more detail. All procedures are detailed under different module headings.

Enumeration Type Documentation

enum _WlzEffFormat

enumeration of the file formats supported. Typedef: WlzEffFormat

Enumerator
WLZEFF_FORMAT_NONE	None, used to indicating no match (equal to zero).
WLZEFF_FORMAT_BMP	Microscoft bitmap.
WLZEFF_FORMAT_DEN	Stanford density.
WLZEFF_FORMAT_ICS	International cytometry standard.
WLZEFF_FORMAT_PNM	Portable any map.
WLZEFF_FORMAT_PIC	Biorad confocal pic format.
WLZEFF_FORMAT_SLC	SLC volume files.
WLZEFF_FORMAT_VFF	Sunvision volumes.
WLZEFF_FORMAT_VTK	Visualization Toolkit.
WLZEFF_FORMAT_WLZ	Woolz.
WLZEFF_FORMAT_IPL	IP Lab.
WLZEFF_FORMAT_TIFF	Tiff.
WLZEFF_FORMAT_RAW	Raw data.
WLZEFF_FORMAT_AM	Amira.
WLZEFF_FORMAT_JPEG	Jpeg.
WLZEFF_FORMAT_ANL	Analyze 7.5.
WLZEFF_FORMAT_GIF	Graphics Interchange Format.
WLZEFF_FORMAT_MESH	Pascal Frey's tetrahedral mesh format.
WLZEFF_FORMAT_NODEELE	Jonathan Shewchuk's mesh format.
WLZEFF_FORMAT_VMESH	GRUMMP tetrahedral mesh format.
WLZEFF_FORMAT_PLY2	Riken PLY2 mesh format.
WLZEFF_FORMAT_OBJ	Wavefront geometry format.
WLZEFF_FORMAT_TXT	Simple ASCII text listing, csv format.
WLZEFF_FORMAT_NIFTI	Neuroimaging Informatics Technology Initiative format based on Analyze 7.5.
WLZEFF_FORMAT_SMESH	GRUMMP surface mesh format.
WLZEFF_FORMAT_EMT	Netgen neutral mesh format.
WLZEFF_FORMAT_STL	Stereolithography file format.
WLZEFF_FORMAT_PVL	Drishti PVL dot NC format.
WLZEFF_FORMAT_NRRD	Utah nearly raw raster data format.
WLZEFF_FORMAT_COUNT	Keep last: Number of formats (including WLZEFF_FORMAT_NONE).

enum _WlzEffAmToken

Tokens for parsing the headers of Amira lattice files. Typedef: WlzEffAmToken.

Enumerator
WLZEFF_AM_TOKEN_NONE
WLZEFF_AM_TOKEN_BOUNDINGBOX
WLZEFF_AM_TOKEN_CLOSE
WLZEFF_AM_TOKEN_COLOR
WLZEFF_AM_TOKEN_COLORMAP
WLZEFF_AM_TOKEN_CONTENT
WLZEFF_AM_TOKEN_COORDTYPE
WLZEFF_AM_TOKEN_DEFINE
WLZEFF_AM_TOKEN_EXPRESSION
WLZEFF_AM_TOKEN_HASH
WLZEFF_AM_TOKEN_ID
WLZEFF_AM_TOKEN_IMAGEDATA
WLZEFF_AM_TOKEN_LATTICE
WLZEFF_AM_TOKEN_MATERIALS
WLZEFF_AM_TOKEN_NAME
WLZEFF_AM_TOKEN_OPEN
WLZEFF_AM_TOKEN_PARAMETERS
WLZEFF_AM_TOKEN_SEEDS
WLZEFF_AM_TOKEN_LIMITS
WLZEFF_AM_TOKEN_TIFF
WLZEFF_AM_TOKEN_TRANSFORM

enum _WlzEffAmDim

Dimension of the data. Typedef: WlzEffAmDim.

Enumerator
WLZEFF_AM_DIM_NONE	Dimension unknown.
WLZEFF_AM_DIM_2	2D.
WLZEFF_AM_DIM_3	3D.

enum _WlzEffAmEndian

Big or little endian binary data. The values endian enum must be kept distinct from the dimension enum values (apart from none). Typedef: WlzEffAmFormat.

Enumerator
WLZEFF_AM_ENDIAN_NONE	Unknown endianness.
WLZEFF_AM_ENDIAN_BIG	Big endian.
WLZEFF_AM_ENDIAN_LITTLE	Little endian.

enum _WlzEffAmFormat

ASCII or binary data. Typedef: WlzEffAmFormat.

Enumerator
WLZEFF_AM_FMT_NONE	Unknown data format.
WLZEFF_AM_FMT_BINARY	Header ascii, Binary data.
WLZEFF_AM_FMT_ASCII	Ascii header and data.

enum _WlzEffAmDatType

Type of data: byte, ... Typedef: WlzEffAmDatType.

Enumerator
WLZEFF_AM_DATTYPE_NONE	Unknown data type.
WLZEFF_AM_DATTYPE_BYTE	Byte (8 bit) data.
WLZEFF_AM_DATTYPE_SHORT	Short (16 bit) data.

enum _WlzEffAmCoordType

Type of coordinate system. Typedef: WlzEffAmCoordType.

Enumerator
WLZEFF_AM_COORDTYPE_NONE	Unknown coordinate type.
WLZEFF_AM_COORDTYPE_UNITFORM	Uniform coordinates.

enum _WlzEffAmLatComp

Type of compression used. Typedef: WlzEffAmLatComp.

Enumerator
WLZEFF_AM_LATCOMP_NONE	No compression.
WLZEFF_AM_LATCOMP_HXBYTERLE	Run length encoded bytes.

enum _WlzEffAmLatType

Type of lattice: uniform, ... Typedef: WlzEffAmLatType.

Enumerator
WLZEFF_AM_LATTYPE_NONE	Unknown lattice type.
WLZEFF_AM_LATTYPE_DATA	Voxel lattice data.
WLZEFF_AM_LATTYPE_LABELS	Domain lattice data.

enum _WlzEffAnlDataType

Valid Analyze data type values. Typedef: WlzEffAnlDataType.

Valid Analyze data type values. Typedef: WlzEffAnlOrient.

Enumerator
WLZEFF_ANL_DT_NONE
WLZEFF_ANL_DT_UNKOWN
WLZEFF_ANL_DT_BINARY
WLZEFF_ANL_DT_UNSIGNED_CHAR
WLZEFF_ANL_DT_SIGNED_SHORT
WLZEFF_ANL_DT_SIGNED_INT
WLZEFF_ANL_DT_FLOAT
WLZEFF_ANL_DT_COMPLEX
WLZEFF_ANL_DT_DOUBLE
WLZEFF_ANL_DT_RGB
WLZEFF_ANL_DT_ALL

Function Documentation

WlzEffFormat WlzEffStringExtToFormat ( const char * extStr )

Returns a file format for the given file extension string.

Returns: File format, WLZEFF_FORMAT_NONE if string not matched.

Parameters

extStr Given file extension string.

References WLZEFF_FORMAT_AM, WLZEFF_FORMAT_ANL, WLZEFF_FORMAT_BMP, WLZEFF_FORMAT_DEN, WLZEFF_FORMAT_EMT, WLZEFF_FORMAT_GIF, WLZEFF_FORMAT_ICS, WLZEFF_FORMAT_IPL, WLZEFF_FORMAT_JPEG, WLZEFF_FORMAT_MESH, WLZEFF_FORMAT_NIFTI, WLZEFF_FORMAT_NODEELE, WLZEFF_FORMAT_NONE, WLZEFF_FORMAT_NRRD, WLZEFF_FORMAT_OBJ, WLZEFF_FORMAT_PIC, WLZEFF_FORMAT_PLY2, WLZEFF_FORMAT_PNM, WLZEFF_FORMAT_PVL, WLZEFF_FORMAT_RAW, WLZEFF_FORMAT_SLC, WLZEFF_FORMAT_SMESH, WLZEFF_FORMAT_STL, WLZEFF_FORMAT_TIFF, WLZEFF_FORMAT_TXT, WLZEFF_FORMAT_VFF, WLZEFF_FORMAT_VMESH, WLZEFF_FORMAT_VTK, WLZEFF_FORMAT_WLZ, and WlzStringMatchValue().

Referenced by WlzEffStringFormatFromFileName().

WlzEffFormat WlzEffStringToFormat ( const char * fmtStr )

Returns a file format for the given file format string.

Returns: File format, WLZEFF_FORMAT_NONE if string not matched.

Parameters

fmtStr Given file format string.

References WLZEFF_FORMAT_AM, WLZEFF_FORMAT_ANL, WLZEFF_FORMAT_BMP, WLZEFF_FORMAT_DEN, WLZEFF_FORMAT_EMT, WLZEFF_FORMAT_GIF, WLZEFF_FORMAT_ICS, WLZEFF_FORMAT_IPL, WLZEFF_FORMAT_JPEG, WLZEFF_FORMAT_MESH, WLZEFF_FORMAT_NIFTI, WLZEFF_FORMAT_NODEELE, WLZEFF_FORMAT_NONE, WLZEFF_FORMAT_NRRD, WLZEFF_FORMAT_OBJ, WLZEFF_FORMAT_PIC, WLZEFF_FORMAT_PLY2, WLZEFF_FORMAT_PNM, WLZEFF_FORMAT_PVL, WLZEFF_FORMAT_RAW, WLZEFF_FORMAT_SLC, WLZEFF_FORMAT_SMESH, WLZEFF_FORMAT_STL, WLZEFF_FORMAT_TIFF, WLZEFF_FORMAT_TXT, WLZEFF_FORMAT_VFF, WLZEFF_FORMAT_VMESH, WLZEFF_FORMAT_VTK, WLZEFF_FORMAT_WLZ, and WlzStringMatchValue().

Referenced by WlzEffBibParseFileRecord().

const char* WlzEffStringFromFormat	(	WlzEffFormat	fileFmt,
		const char **	dstExtStr
	)

Returns a string which is suitable for displaying the given format and sets a destination pointer for the formats file extension.

Returns: String appropriate to format, or NULL on error.

Parameters

fileFmt	Given file format.
dstExtStr	Destination ptr for extension string.

References WLZEFF_FORMAT_AM, WLZEFF_FORMAT_ANL, WLZEFF_FORMAT_BMP, WLZEFF_FORMAT_DEN, WLZEFF_FORMAT_EMT, WLZEFF_FORMAT_GIF, WLZEFF_FORMAT_ICS, WLZEFF_FORMAT_IPL, WLZEFF_FORMAT_JPEG, WLZEFF_FORMAT_MESH, WLZEFF_FORMAT_NIFTI, WLZEFF_FORMAT_NODEELE, WLZEFF_FORMAT_NRRD, WLZEFF_FORMAT_OBJ, WLZEFF_FORMAT_PIC, WLZEFF_FORMAT_PLY2, WLZEFF_FORMAT_PNM, WLZEFF_FORMAT_PVL, WLZEFF_FORMAT_RAW, WLZEFF_FORMAT_SLC, WLZEFF_FORMAT_SMESH, WLZEFF_FORMAT_STL, WLZEFF_FORMAT_TIFF, WLZEFF_FORMAT_TXT, WLZEFF_FORMAT_VFF, WLZEFF_FORMAT_VMESH, WLZEFF_FORMAT_VTK, and WLZEFF_FORMAT_WLZ.

Referenced by WlzEffBibWriteFileRecord(), and WlzEffFormatTable().

WlzEffFormat WlzEffStringFormatFromFileName ( const char * fNameStr )

Returns a the file format implied by the file extension used in the given file name. If no match is found WlzEffFormat::WLZEFF_FORMAT_NONE is returned.

Returns: File format.

Parameters

fNameStr Given file name.

References WLZEFF_FORMAT_NONE, and WlzEffStringExtToFormat().

WlzObject* WlzEffReadObj	(	FILE *	fP,
		const char *	fName,
		WlzEffFormat	fFmt,
		int	split,
		int	sTrans,
		int	gTrans,
		WlzErrorNum *	dstErr
	)

Reads a woolz object from the the given file names(s) or opened file, where the file format is that given as a parameter. The ANL, ICS, PNM (and a few other multi file formats) require a file name, for all other formats either the file name or a file pointer may be given.

Returns: Woolz object read from file, or NULL on error.

Parameters

fP	Input file.
fName	File name (and path).
fFmt	File format.
split	If non zero and the file contains a index labeled image then the image is split into seperate domains.
sTrans	If non zero and the file contains a spatial transform then the image is transformed otherwise a WLZ_TRANS_OBJ may be returned.
gTrans	If non zero and the file contains a grey transform then the image is transformed.
dstErr	Destination error number ptr, may be NULL.

References WLZ_ERR_NONE, WLZ_ERR_PARAM_DATA, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZEFF_FORMAT_AM, WLZEFF_FORMAT_ANL, WLZEFF_FORMAT_BMP, WLZEFF_FORMAT_DEN, WLZEFF_FORMAT_EMT, WLZEFF_FORMAT_GIF, WLZEFF_FORMAT_ICS, WLZEFF_FORMAT_IPL, WLZEFF_FORMAT_JPEG, WLZEFF_FORMAT_MESH, WLZEFF_FORMAT_NIFTI, WLZEFF_FORMAT_NODEELE, WLZEFF_FORMAT_NRRD, WLZEFF_FORMAT_OBJ, WLZEFF_FORMAT_PIC, WLZEFF_FORMAT_PLY2, WLZEFF_FORMAT_PNM, WLZEFF_FORMAT_PVL, WLZEFF_FORMAT_SLC, WLZEFF_FORMAT_SMESH, WLZEFF_FORMAT_STL, WLZEFF_FORMAT_TIFF, WLZEFF_FORMAT_VFF, WLZEFF_FORMAT_VMESH, WLZEFF_FORMAT_VTK, WLZEFF_FORMAT_WLZ, WlzEffReadObjAm(), WlzEffReadObjAnl(), WlzEffReadObjBmp(), WlzEffReadObjDen(), WlzEffReadObjEMT(), WlzEffReadObjGif(), WlzEffReadObjIcs(), WlzEffReadObjIPL(), WlzEffReadObjJpeg(), WlzEffReadObjMesh(), WlzEffReadObjNifti(), WlzEffReadObjNodeEle(), WlzEffReadObjNrrd(), WlzEffReadObjObj(), WlzEffReadObjPic(), WlzEffReadObjPly2(), WlzEffReadObjPnm(), WlzEffReadObjPvl(), WlzEffReadObjSlc(), WlzEffReadObjSMesh(), WlzEffReadObjStl(), WlzEffReadObjTiff(), WlzEffReadObjVff(), WlzEffReadObjVMesh(), WlzEffReadObjVtk(), and WlzReadObj().

WlzErrorNum WlzEffWriteObj	(	FILE *	fP,
		const char *	fName,
		WlzObject *	obj,
		WlzEffFormat	fFmt
	)

Writes a woolz object to the the given file stream, with the given file format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
fName	File name (and path).
obj	Given Woolz object.
fFmt	File format.

References WLZ_ERR_NONE, WLZ_ERR_PARAM_DATA, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_UNIMPLEMENTED, WLZ_ERR_WRITE_EOF, WLZEFF_FORMAT_AM, WLZEFF_FORMAT_ANL, WLZEFF_FORMAT_BMP, WLZEFF_FORMAT_DEN, WLZEFF_FORMAT_EMT, WLZEFF_FORMAT_GIF, WLZEFF_FORMAT_ICS, WLZEFF_FORMAT_IPL, WLZEFF_FORMAT_JPEG, WLZEFF_FORMAT_MESH, WLZEFF_FORMAT_NIFTI, WLZEFF_FORMAT_NODEELE, WLZEFF_FORMAT_NRRD, WLZEFF_FORMAT_OBJ, WLZEFF_FORMAT_PIC, WLZEFF_FORMAT_PLY2, WLZEFF_FORMAT_PNM, WLZEFF_FORMAT_PVL, WLZEFF_FORMAT_SLC, WLZEFF_FORMAT_SMESH, WLZEFF_FORMAT_STL, WLZEFF_FORMAT_TIFF, WLZEFF_FORMAT_TXT, WLZEFF_FORMAT_VFF, WLZEFF_FORMAT_VMESH, WLZEFF_FORMAT_VTK, WLZEFF_FORMAT_WLZ, WlzEffWriteObjAm(), WlzEffWriteObjAnl(), WlzEffWriteObjBmp(), WlzEffWriteObjDen(), WlzEffWriteObjEMT(), WlzEffWriteObjIcs(), WlzEffWriteObjIPL(), WlzEffWriteObjJpeg(), WlzEffWriteObjMesh(), WlzEffWriteObjNifti(), WlzEffWriteObjNodeEle(), WlzEffWriteObjNrrd(), WlzEffWriteObjObj(), WlzEffWriteObjPic(), WlzEffWriteObjPly2(), WlzEffWriteObjPnm(), WlzEffWriteObjPvl(), WlzEffWriteObjSlc(), WlzEffWriteObjSMesh(), WlzEffWriteObjStl(), WlzEffWriteObjTiff(), WlzEffWriteObjTxt(), WlzEffWriteObjVff(), WlzEffWriteObjVMesh(), WlzEffWriteObjVtk(), and WlzWriteObj().

int WlzEffNumberOfFormats ( void )

Retuns the number of file formats, ie WLZEFF_FORMAT_COUNT - 1.

Returns: Number of file formats.

References WLZEFF_FORMAT_COUNT.

char* WlzEffFormatTable	(	unsigned	indWth,
		unsigned	desWth,
		unsigned	extWth,
		WlzErrorNum *	dstErr
	)

Creates an ascii table of the valid formats supported by WlzExtFF. This may be useful for giving usage information in binaries.

Returns: Ascii table of valid file formats.

Parameters

indWth	Indent width (no default).
desWth	Maximum description width (if 0 a default field width is used).
extWth	Maximum extension width (if 0 a default field width is used).
dstErr	Destination error pointer, may be NULL.

References AlcFree(), AlcMalloc(), WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZEFF_FORMAT_COUNT, and WlzEffStringFromFormat().

WlzObject* WlzEffReadObjAm	(	FILE *	fP,
		int	split,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given file using the Amira lattice (.am file) format.

Returns: New Woolz object read from file.

Parameters

fP	Input file pointer.
split	Split label lattice files into a compound object of domains if non zero.
dstErr	Destination pointer for error number, may be NULL.

References Alc3Free(), _WlzEffAmHead::latType, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_READ_INCOMPLETE, WlzAssignObject(), WLZEFF_AM_LATTYPE_DATA, WLZEFF_AM_LATTYPE_LABELS, and WlzFreeObj().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjAm	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file using the Amira lattice (.am file) format.

Returns: Woolz error code.

Parameters

fP	Output file pointer
obj	Object to be written.

References Alc3Free(), ALC_ER_NONE, AlcCalloc(), AlcChar3Malloc(), AlcDLPListEntryAppend(), AlcFree(), AlcMalloc(), AlcShort3Malloc(), AlcStrDup(), _WlzEffAmHead::bBox, _WlzEffAmMaterial::color, _WlzEffAmHead::coordType, _WlzValues::core, _WlzDomain::core, _WlzProperty::core, _WlzEffAmHead::dim, _WlzObject::domain, _WlzEffAmHead::endian, _WlzEffAmHead::fmt, _WlzProperty::greyV, _WlzEffAmMaterial::id, _WlzEffAmHead::imageData, _WlzGreyV::inv, _WlzEffAmHead::latBytes, _WlzEffAmHead::latComp, _WlzEffAmHead::latDatType, _WlzEffAmHead::latLabel, _WlzEffAmHead::latSize, _WlzEffAmHead::latType, _WlzPropertyList::list, _WlzEffAmHead::matCount, _WlzEffAmHead::materials, _WlzEffAmMaterial::name, _WlzProperty::name, _WlzEffAmMaterial::next, _WlzCompoundArray::o, _WlzDomain::p, _WlzEffAmMaterial::prev, _WlzGreyV::rgbv, _WlzPixelV::type, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzKrigModelFn::type, _WlzPixelV::v, _WlzObject::values, _WlzEffAmHead::versionMajor, _WlzEffAmHead::versionMinor, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzDVertex3::vtX, _WlzIVertex3::vtY, _WlzDVertex3::vtY, _WlzIVertex3::vtZ, _WlzDVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_COMPOUND_ARR_1, WLZ_EFF_AM_LABEL_MAXC, WLZ_EFF_AM_REC_MAXC, WLZ_EMPTY_OBJ, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_GREY_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_ERR_UNIMPLEMENTED, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_INT, WLZ_GREY_RGBA, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_THRESH_HIGH, WLZ_VOXELVALUETABLE_GREY, WlzAssignObject(), WlzBoundingBox3I(), WlzDiffDomain(), WLZEFF_AM_COORDTYPE_NONE, WLZEFF_AM_COORDTYPE_UNITFORM, WLZEFF_AM_DATTYPE_BYTE, WLZEFF_AM_DATTYPE_NONE, WLZEFF_AM_DATTYPE_SHORT, WLZEFF_AM_DIM_2, WLZEFF_AM_DIM_3, WLZEFF_AM_DIM_NONE, WLZEFF_AM_ENDIAN_BIG, WLZEFF_AM_ENDIAN_LITTLE, WLZEFF_AM_FMT_ASCII, WLZEFF_AM_FMT_BINARY, WLZEFF_AM_FMT_NONE, WLZEFF_AM_LATCOMP_HXBYTERLE, WLZEFF_AM_LATCOMP_NONE, WLZEFF_AM_LATTYPE_DATA, WLZEFF_AM_LATTYPE_LABELS, WLZEFF_AM_LATTYPE_NONE, WLZEFF_AM_TOKEN_BOUNDINGBOX, WLZEFF_AM_TOKEN_COLOR, WLZEFF_AM_TOKEN_COLORMAP, WLZEFF_AM_TOKEN_CONTENT, WLZEFF_AM_TOKEN_COORDTYPE, WLZEFF_AM_TOKEN_DEFINE, WLZEFF_AM_TOKEN_EXPRESSION, WLZEFF_AM_TOKEN_HASH, WLZEFF_AM_TOKEN_ID, WLZEFF_AM_TOKEN_IMAGEDATA, WLZEFF_AM_TOKEN_LATTICE, WLZEFF_AM_TOKEN_LIMITS, WLZEFF_AM_TOKEN_MATERIALS, WLZEFF_AM_TOKEN_NAME, WLZEFF_AM_TOKEN_NONE, WLZEFF_AM_TOKEN_PARAMETERS, WLZEFF_AM_TOKEN_SEEDS, WLZEFF_AM_TOKEN_TIFF, WLZEFF_AM_TOKEN_TRANSFORM, WlzFreeObj(), WlzFreePropertyList(), WlzFreePropertyListEntry(), WlzFromArray3D(), WlzGreyTypeFromObj(), WlzIsEmpty(), WlzMakeCompoundArray(), WlzMakeGreyProperty(), WlzMakeMain(), WlzMakeNameProperty(), WlzMakePropertyList(), WlzStringMatchValue(), WlzThreshold(), WlzToArray3D(), WlzVozelSz(), _WlzIBox3::xMax, _WlzDBox3::xMax, _WlzIBox3::xMin, _WlzDBox3::xMin, _WlzIBox3::yMax, _WlzDBox3::yMax, _WlzIBox3::yMin, _WlzDBox3::yMin, _WlzIBox3::zMax, _WlzDBox3::zMax, _WlzIBox3::zMin, and _WlzDBox3::zMin.

Referenced by WlzEffWriteObj().

WlzErrorNum WlzEffAnlFileNames	(	char **	fileBody,
		char **	hdrFileName,
		char **	imgFileName,
		const char *	gvnFileName
	)

Builds the ANALYZE file names from the given file name. These strings should be free'd using AlcFree() when no longer required.

Returns: Woolz error code.

Parameters

fileBody	Dest ptr for the file body.
hdrFileName	Dest ptr for the '.hdr' file name.
imgFileName	Dest ptr for the '.img' file name.
gvnFileName	Given file name with '.hdr', '.img' or no extension.

References AlcMalloc(), WLZ_ERR_MEM_ALLOC, and WLZ_ERR_NONE.

Referenced by WlzEffReadObjAnl(), and WlzEffWriteObjAnl().

WlzObject* WlzEffReadObjAnl	(	const char *	gvnFileName,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the ANALYZE 7.5 format. The given file name is used to generate the '.hdr' and '.img' filenames.

Returns: New Woolz object or NULL on error.

Parameters

gvnFileName	Given file name.
dstErr	Destination error code, may be NULL.

References AlcFree(), _WlzEffAnlImageDim::bitPix, _WlzEffAnlImageDim::dataType, _WlzGreyV::dbv, _WlzEffAnlImageDim::dim, _WlzEffAnlDsr::dim, _WlzGreyV::flv, _WlzEffAnlDsr::hk, _WlzVertex::i2, _WlzVertex::i3, _WlzGreyV::inv, _WlzCompoundArray::o, _WlzEffAnlHeaderKey::regular, _WlzGreyV::shv, _WlzPixelV::type, _WlzGreyV::ubv, _WlzPixelV::v, _WlzIVertex2::vtX, _WlzIVertex3::vtX, _WlzIVertex2::vtY, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_ERR_GREY_TYPE, WLZ_ERR_NONE, WLZ_ERR_OBJECT_DATA, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_GREY_DOUBLE, WLZ_GREY_ERROR, WLZ_GREY_FLOAT, WLZ_GREY_INT, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WlzAssignObject(), WLZEFF_ANL_DT_DOUBLE, WLZEFF_ANL_DT_FLOAT, WLZEFF_ANL_DT_SIGNED_INT, WLZEFF_ANL_DT_SIGNED_SHORT, WLZEFF_ANL_DT_UNSIGNED_CHAR, WlzEffAnlFileNames(), WlzFreeObj(), WlzMakeCompoundArray(), WlzMakeCuboid(), and WlzMakeRect().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjAnl	(	const char *	gvnFileName,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file(s) using the ANALYZE 7.5 file format. The given file name is used to generate the '.hdr' and '.img' filenames.

Returns: Woolz error code.

Parameters

gvnFileName	Given file name with .hdr, .img or no extension.
obj	Given woolz object.

Referenced by WlzEffWriteObj().

WlzThreeDViewStruct* WlzEffBibRead3DView	(	FILE *	fP,
		char **	dstMsg,
		WlzErrorNum *	dstErr
	)

Reads a 3D view from the given file pointer.

Returns: New view.

Parameters

fP	Given file pointer.
dstMsg	Destination pointer for bibfile parsing error message strings, may be NULL.
dstErr	Destination error pointer, may be NULL.

References BIBFILE_ER_NONE, BibFileRecordFree(), BibFileRecordRead(), BibFileRecord::name, WLZ_3D_VIEW_STRUCT, WLZ_ERR_NONE, WLZ_ERR_READ_INCOMPLETE, WlzEffBibParse3DSectionViewParamsRecord(), and WlzMake3DViewStruct().

WlzErrorNum WlzEffBibWrite3DSectionViewParamsRecord	(	FILE *	fp,
		char *	recordName,
		WlzThreeDViewStruct *	wlzViewStr
	)

Write the section view parameters in the bibtex style record using the bibFile library.

Returns: woolz error number

Parameters

fp	FILE pointer opened for writing
recordName	record name
wlzViewStr	woolz 3D view structure

Source:: WlzExtFFBibUtils.c

References BIBFILE_ER_NONE, BibFileFieldMakeVa(), BibFileRecordFree(), BibFileRecordMake(), BibFileRecordWrite(), _WlzThreeDViewStruct::dist, _WlzThreeDViewStruct::fixed, _WlzThreeDViewStruct::phi, _WlzThreeDViewStruct::scale, _WlzThreeDViewStruct::theta, _WlzThreeDViewStruct::up, _WlzThreeDViewStruct::view_mode, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_ERR_NONE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_M_PI, WLZ_STATUE_MODE, WLZ_UP_IS_UP_MODE, WLZ_ZETA_MODE, and _WlzThreeDViewStruct::zeta.

Referenced by main().

WlzErrorNum WlzEffBibParse3DSectionViewParamsRecord	(	BibFileRecord *	bibfileRecord,
		WlzThreeDViewStruct *	wlzViewStr
	)

Parse the bibfile record for a woolz 3D view structure setting paramters in the given view structure.

Returns: woolz error number

Parameters

bibfileRecord	bibfile record as read using libbibFile
wlzViewStr	woolz 3D view structure already allocated

Source:: WlzExtFFBibUtils.c

Referenced by main(), and WlzEffBibRead3DView().

WlzErrorNum WlzEffBibWriteWarpTransformParamsRecord	(	FILE *	fp,
		char *	recordName,
		WlzFnType	basisFnType,
		WlzTransformType	affineType,
		WlzMeshGenMethod	meshMthd,
		int	meshMinDst,
		int	meshMaxDst
	)

Write the details of a warp transformation parameters. Note this does not write the warp transformation itself.

Returns: woolz error number

Parameters

fp	FILE pointer opened for writing
recordName	record name
basisFnType	interpolation or basis function type
affineType	Affine transform type (rigid-body, full affine etc.)
meshMthd	method used to define the mesh
meshMinDst	mesh minimum distance
meshMaxDst	mesh maximum distance

Source:: WlzExtFFBibUtils.c

References BIBFILE_ER_NONE, BibFileFieldMakeVa(), BibFileRecordFree(), BibFileRecordMake(), BibFileRecordWrite(), WLZ_ERR_NONE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_FN_BASIS_2DCONF_POLY, WLZ_FN_BASIS_2DGAUSS, WLZ_FN_BASIS_2DMQ, WLZ_FN_BASIS_2DPOLY, WLZ_FN_BASIS_2DTPS, WLZ_MESH_GENMETHOD_BLOCK, WLZ_MESH_GENMETHOD_GRADIENT, WLZ_TRANSFORM_2D_AFFINE, WLZ_TRANSFORM_2D_NOSHEAR, and WLZ_TRANSFORM_2D_REG.

Referenced by main().

WlzErrorNum WlzEffBibParseWarpTransformParamsRecord	(	BibFileRecord *	bibfileRecord,
		WlzFnType *	basisFnType,
		WlzTransformType *	affineType,
		WlzMeshGenMethod *	meshMthd,
		int *	meshMinDst,
		int *	meshMaxDst
	)

Parse the bibfile record for the warp transformation parameter settings.

Returns: Woolz error number

Parameters

bibfileRecord	bibfile record as read by libbibFile
basisFnType	return for basis function type
affineType	Affine transform type (rigid-body, full affine etc.)
meshMthd	return for mesh method type
meshMinDst	return for mesh minimum distance
meshMaxDst	return for mesh maximum distance

Source:: WlzExtFFBibUtils.c

References BibFileFieldParseFmt(), BibFileRecord::field, _BibFileField::name, _BibFileField::next, _BibFileField::value, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_FN_BASIS_2DCONF_POLY, WLZ_FN_BASIS_2DGAUSS, WLZ_FN_BASIS_2DMQ, WLZ_FN_BASIS_2DPOLY, WLZ_FN_BASIS_2DTPS, WLZ_MESH_GENMETHOD_BLOCK, WLZ_MESH_GENMETHOD_GRADIENT, WLZ_TRANSFORM_2D_AFFINE, WLZ_TRANSFORM_2D_NOSHEAR, and WLZ_TRANSFORM_2D_REG.

WlzErrorNum WlzEffBibWriteTiePointVtxsRecord	(	FILE *	fp,
		char *	recordName,
		int	index,
		WlzDVertex3	dstVtx,
		WlzDVertex3	srcVtx,
		int	relativeFlg
	)

Write a tie-point record in bibtex style.

Returns: Woolz error number

Parameters

fp	FILE pointer opened for writing
recordName	record name
index	index of the given tie points
dstVtx	destination vertex
srcVtx	source vertex
relativeFlg	Non-zero for relative bib coordinates.

Source:: WlzExtFFBibUtils.c

References BIBFILE_ER_NONE, BibFileFieldMakeVa(), BibFileRecordFree(), BibFileRecordMake(), BibFileRecordWrite(), _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_ERR_NONE, and WLZ_ERR_WRITE_INCOMPLETE.

WlzErrorNum WlzEffBibParseTiePointVtxsRecord	(	BibFileRecord *	bibfileRecord,
		int *	index,
		WlzDVertex3 *	dstVtx,
		WlzDVertex3 *	srcVtx,
		int *	relativeFlg
	)

Parse the bibfile record for a tie-point pair of vertices. The record should also include an index so that tie-point ordering is preserved.

Returns: Woolz error number

Parameters

bibfileRecord	bibfile record as read in by libbibFile
index	return for tie-point pair index within list
dstVtx	return for destination vertex
srcVtx	return for source vertex
relativeFlg	return for relative coordinates, non-zero if relative

Source:: WlzExtFFBibUtils.c

References BibFileFieldParseFmt(), BibFileRecord::field, _BibFileField::name, _BibFileField::next, _BibFileField::value, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, and WLZ_ERR_READ_INCOMPLETE.

WlzErrorNum WlzEffBibWriteFileRecord	(	FILE *	fp,
		char *	recordName,
		char *	fileName,
		WlzEffFormat	fileType
	)

Write a bibfile record to record the file name and file type.

Returns: woolz error number

Parameters

fp	FILE pointer
recordName	record name
fileName	file name to be recorded
fileType	file type e.g. image format

Source:: WlzExtFFBibUtils.c

References BIBFILE_ER_NONE, BibFileFieldMakeVa(), BibFileRecordFree(), BibFileRecordMake(), BibFileRecordWrite(), WLZ_ERR_NONE, WLZ_ERR_PARAM_DATA, WLZ_ERR_WRITE_INCOMPLETE, and WlzEffStringFromFormat().

Referenced by main().

WlzErrorNum WlzEffBibParseFileRecord	(	BibFileRecord *	bibfileRecord,
		int *	dstIndex,
		char **	dstFileName,
		WlzEffFormat *	dstFileType
	)

Parse a bibfile record for a filename and type.

Returns: woolz error

Parameters

bibfileRecord	bibfile record as read in by libbibFile
dstIndex	Destination pointer for integer parsed from the record ID, may be NULL.
dstFileName	Destination pointer for file name, may be NULL.
dstFileType	Destination pointer for the file type, may be NULL.

Source:: WlzExtFFBibUtils.c

References AlcStrDup(), BibFileFieldParseFmt(), BibFileRecord::field, BibFileRecord::id, _BibFileField::name, _BibFileField::next, _BibFileField::value, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, and WlzEffStringToFormat().

WlzErrorNum WlzEffBibWriteWarpInputSegmentationParamsRecord	(	FILE *	fp,
		char *	recordName,
		int	normFlg,
		int	histoFlg,
		int	shadeFlg,
		int	gaussFlg,
		double	width
	)

Write a warp segmentation parameter record i.e. the image processing operations and paramters for extracting the gene-expression domain.

Returns: woolz error

Parameters

fp	FILE pointer opened for writing
recordName	bibfile record name
normFlg	normalisation flag
histoFlg	histogram equalise flag
shadeFlg	shade correct flag
gaussFlg	gauss smoothing flag
width	gauss smoothing width parameter

Source:: WlzExtFFBibUtils.c

References BIBFILE_ER_NONE, BibFileFieldMakeVa(), BibFileRecordFree(), BibFileRecordMake(), BibFileRecordWrite(), WLZ_ERR_NONE, and WLZ_ERR_WRITE_INCOMPLETE.

WlzErrorNum WlzEffBibParseWarpInputSegmentationParamsRecord	(	BibFileRecord *	bibfileRecord,
		int *	normFlg,
		int *	histoFlg,
		int *	shadeFlg,
		int *	gaussFlg,
		double *	width,
		int *	threshLow,
		int *	threshHigh
	)

Parse the bibfile record for a MAPaint WarpInputSegmentationParams record.

Returns: woolz error

Parameters

bibfileRecord	bibfile record as read by libbibFile
normFlg	normalisation flag
histoFlg	histogram equalise flag
shadeFlg	shade correct flag
gaussFlg	gauss smoothing flag
width	gauss smoothing width
threshLow	low threshold value
threshHigh	high threshold value

Source:: WlzExtFFBibUtils.c

References BibFileFieldParseFmt(), BibFileRecord::field, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, and WLZ_ERR_READ_INCOMPLETE.

WlzObject* WlzEffReadObjBmp	(	const char *	gvnFileName,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given file(s) using the '.pnm' file format.

Returns: Object read from file.

Parameters

gvnFileName	Given file name.
dstErr	Dst error pointer, may be NULL.

References WLZ_ERR_NONE, WLZEFF_FORMAT_BMP, and WlzEffReadObjStack().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjBmp	(	const char *	gvnFileName,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file(s) using the '.pnm' file format.

Returns: Woolz error number.

Parameters

gvnFileName	Given file name.
obj	Given woolz object.

References WLZ_ERR_NONE, WLZEFF_FORMAT_BMP, and WlzEffWriteObjStack().

Referenced by WlzEffWriteObj().

WlzErrorNum WlzEffWriteObjBmp2D	(	const char *	fNameStr,
		WlzObject *	obj,
		WlzIVertex2	imgSz,
		WlzIVertex2	imgOrg,
		unsigned char *	data,
		unsigned char	bgd
	)

Writes the given 2D Woolz object to the given file using the '.pnm' file format.

Returns: Woolz error number.

Parameters

fNameStr	Given file name.
obj	Given woolz object.
imgSz	Required image size.
imgOrg	Required image origin.
data	Buffer of imgSz bytes.
bgd	Background value.

Referenced by WlzEffWriteObjStack().

WlzErrorNum WlzEffReadObjBmpData2D	(	FILE *	fP,
		WlzIVertex2 *	gvnImgSz,
		unsigned char ***	data
	)

Reads the data from a pgm file into the data array given.

Returns: Woolz error number.

Parameters

fP	Given file stream.
gvnImgSz	Dst ptr for image size which is assumed valid if height and width are non zero.
data	Ptr to 2D array for data.

Referenced by WlzEffWriteObjStack().

WlzObject* WlzEffReadObjDen	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the Stanford density file format.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References ALC_ER_NONE, AlcUnchar3Free(), AlcUnchar3Malloc(), _WlzObject::domain, _WlzEffDenHeader::extrLen, _WlzEffDenHeader::extrMax, _WlzEffDenHeader::extrMin, _WlzEffDenHeader::mapLen, _WlzEffDenHeader::mapLength, _WlzEffDenHeader::mapMax, _WlzEffDenHeader::mapMin, _WlzEffDenHeader::mapWarps, _WlzEffDenHeader::orgLen, _WlzEffDenHeader::orgMax, _WlzEffDenHeader::orgMin, _WlzDomain::p, _WlzEffDenHeader::version, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_GREY_UBYTE, WLZEFF_DEN_VERSION, and WlzFromArray3D().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjDen	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the Stanford density file format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcUnchar3Free(), _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzEffDenHeader::extrLen, _WlzEffDenHeader::extrMax, _WlzEffDenHeader::extrMin, _WlzPlaneDomain::kol1, _WlzPlaneDomain::lastkl, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzPlaneDomain::line1, _WlzEffDenHeader::mapLen, _WlzEffDenHeader::mapLength, _WlzEffDenHeader::mapMax, _WlzEffDenHeader::mapMin, _WlzEffDenHeader::mapWarps, _WlzEffDenHeader::orgLen, _WlzEffDenHeader::orgMax, _WlzEffDenHeader::orgMin, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzObject::values, _WlzEffDenHeader::version, _WlzIVertex3::vtX, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_UBYTE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, WLZEFF_DEN_VERSION, and WlzToArray3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjEMT	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the GRUMMP vmesh tetrahedral mesh file format.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References AlcFree(), AlcMalloc(), AlcVectorExtendAndGet(), AlcVectorItemGet(), _WlzCMesh3D::bBox, _WlzDomain::cm3, _WlzValues::core, _WlzCMeshRes::elm, _WlzCMeshRes::nod, _WlzCMesh3D::res, _WlzCMeshEntRes::vec, WLZ_CMESH_3D, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WlzBoundingBoxVtx3D(), WlzCMeshDelUnusedNodes3D(), WlzCMeshFree3D(), WlzCMeshNew3D(), WlzCMeshNewElm3D(), WlzCMeshNewNod3D(), WlzCMeshReassignGridCells3D(), WlzCMeshUpdateMaxSqEdgLen3D(), and WlzMakeMain().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjEMT	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the Netgen neutral mesh file format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcFree(), AlcMalloc(), AlcVectorItemGet(), _WlzDomain::cm3, _WlzDomain::core, _WlzObject::domain, _WlzCMeshFace::edu, _WlzCMeshRes::elm, _WlzCMeshElm3D::face, _WlzCMeshNod3D::idx, _WlzCMeshElm3D::idx, _WlzCMeshEntRes::maxEnt, _WlzCMeshEdgU3D::next, _WlzCMeshEdgU3D::nod, _WlzCMeshRes::nod, _WlzCMeshEntRes::numEnt, _WlzCMeshFace::opp, _WlzCMeshNod3D::pos, _WlzCMesh3D::res, _WlzObject::type, _WlzCMesh3D::type, _WlzCMeshEntRes::vec, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_3D, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_WRITE_INCOMPLETE, and WlzCMeshElmGetNodes3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjGif	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the file pointer using the '.gif' file format. This function currently has the following limitations:

Returns: Object read from file.

the aspect ratio of the pixels. is ignored.
only the first frame of an animated GIF is read.
transparency is ignored.

Parameters

fP	File pointer.
dstErr	Destination error pointer, may be NULL.

References Alc2Free(), ALC_ER_NONE, AlcCalloc(), AlcFree(), AlcInt2Malloc(), _WlzEffGifScreen::AspectRatio, _WlzEffGifScreen::Background, _WlzEffGifScreen::BitPixel, BitSet, _WlzEffGifLWZWSp::clrCode, _WlzEffGifLWZWSp::codeSz, _WlzEffGifScreen::ColorMap, _WlzEffGifScreen::ColorResolution, _WlzEffGif89::delayTime, _WlzEffGif89::disposal, _WlzEffGifLWZWSp::endCode, _WlzEffGifLWZWSp::fresh, _WlzEffGifLWZWSp::fstCode, _WlzEffGifScreen::Height, _WlzEffGif89::inputFlag, LM_to_uint, _WlzEffGifLWZWSp::maxCode, _WlzEffGifLWZWSp::maxCodeSz, _WlzEffGifLWZWSp::oldCode, _WlzEffGifLWZWSp::setCodeSz, _WlzEffGifLWZWSp::sp, _WlzEffGifLWZWSp::stack, _WlzEffGifLWZWSp::table, _WlzEffGif89::transparent, _WlzIVertex2::vtX, _WlzIVertex2::vtY, _WlzEffGifScreen::Width, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_READ_INCOMPLETE, WLZ_GREY_RGBA, WLZ_RGBA_RGBA_SET, WLZEFF_GIF_BUFSZ, WLZEFF_GIF_CM_BLUE, WLZEFF_GIF_CM_GREEN, WLZEFF_GIF_CM_RED, WLZEFF_GIF_INTERLACE, WLZEFF_GIF_LOCALCMAP, WLZEFF_GIF_MAXCMAPSZ, WLZEFF_GIF_MAXLWZBITS, and WlzFromArray2D().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffIcsFileNames	(	char **	fileBody,
		char **	icsFileName,
		char **	idsFileName,
		const char *	gvnFileName
	)

Builds the ics file names from the given file name. These strings should be free'd using AlcFree() when no longer required.

Returns: Woolz error number.

Parameters

fileBody	Dest ptr for the file body.
icsFileName	Dest ptr for the '.ics' file name.
idsFileName	Dest ptr for the '.ids' file name.
gvnFileName	Given file name with .ics, .ids or no extension.

References AlcMalloc(), WLZ_ERR_MEM_ALLOC, and WLZ_ERR_NONE.

Referenced by WlzEffReadObjIcs(), and WlzEffWriteObjIcs().

WlzObject* WlzEffReadObjIcs	(	const char *	gvnFileName,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from a pair of files using the ICS format. The given file name is used to generate the '.ics' and '.ids' filenames.

Returns: Object read from file.

Parameters

gvnFileName	Given file name.
dstErr	Destination error number ptr, may be NULL.

References Alc3Free(), ALC_ER_NONE, AlcFree(), AlcInt3Malloc(), AlcShort3Malloc(), AlcUnchar3Malloc(), _WlzEffIcsHeader::coords, _WlzObject::domain, _WlzEffIcsHeader::format, _WlzEffIcsHeader::order, _WlzDomain::p, _WlzEffIcsHeader::parameters, _WlzEffIcsHeader::scil, _WlzEffIcsHeader::sigBits, _WlzEffIcsHeader::sign, _WlzEffIcsHeader::sizes, _WlzEffIcsHeader::versionMajor, _WlzEffIcsHeader::versionMinor, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_READ_INCOMPLETE, WLZ_GREY_ERROR, WLZ_GREY_INT, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZEFF_ICS_PARAMETERS_MAX, WLZEFF_ICS_REC_LEN_MAX, WLZEFF_ICS_TKN_BITS, WLZEFF_ICS_TKN_COORDS, WLZEFF_ICS_TKN_FILENAME, WLZEFF_ICS_TKN_FLOAT, WLZEFF_ICS_TKN_FORMAT, WLZEFF_ICS_TKN_G3D, WLZEFF_ICS_TKN_INT, WLZEFF_ICS_TKN_L3D, WLZEFF_ICS_TKN_LAYOUT, WLZEFF_ICS_TKN_NONE, WLZEFF_ICS_TKN_ORDER, WLZEFF_ICS_TKN_PARAMETERS, WLZEFF_ICS_TKN_REPRESENTATION, WLZEFF_ICS_TKN_SCIL, WLZEFF_ICS_TKN_SIGBITS, WLZEFF_ICS_TKN_SIGN, WLZEFF_ICS_TKN_SIGNED, WLZEFF_ICS_TKN_SIZES, WLZEFF_ICS_TKN_UNSIGNED, WLZEFF_ICS_TKN_VERSION, WLZEFF_ICS_TKN_VIDEO, WLZEFF_ICS_TKN_X, WLZEFF_ICS_TKN_Y, WLZEFF_ICS_TKN_Z, WLZEFF_ICS_VERSION_MAJOR, WLZEFF_ICS_VERSION_MINOR, WlzEffIcsFileNames(), WlzFromArray3D(), and WlzStringMatchValue().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjIcs	(	const char *	gvnFileName,
		WlzObject *	obj
	)

Writes the given Woolz object to a pair of files using the ICS format. The given file name is used to generate the '.ics' and '.ids' filenames.

Returns: Woolz error number.

Parameters

gvnFileName	Given file name with .ics, .ids or no extension.
obj	Given woolz object.

References AlcFree(), AlcUnchar3Free(), _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzPlaneDomain::kol1, _WlzPlaneDomain::lastkl, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzPlaneDomain::line1, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzObject::values, _WlzIVertex3::vtX, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_EOF, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_UBYTE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, WLZEFF_ICS_VERSION_MAJOR, WLZEFF_ICS_VERSION_MINOR, WlzEffIcsFileNames(), and WlzToArray3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjIPL	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the '.ipl' file format.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References Alc3Free(), ALC_ER_NONE, AlcFloat3Malloc(), AlcFree(), AlcInt3Malloc(), AlcShort3Malloc(), AlcUnchar3Malloc(), _WlzObject::domain, _WlzEffIPLHeader::dType, _WlzEffIPLHeader::nFrames, _WlzEffIPLHeader::nHeight, _WlzEffIPLHeader::nWidth, _WlzDomain::p, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_PARAM_TYPE, WLZ_ERR_READ_INCOMPLETE, WLZ_GREY_FLOAT, WLZ_GREY_INT, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZEFF_IPL_TYPE_COL_16, WLZEFF_IPL_TYPE_COL_24, WLZEFF_IPL_TYPE_FLOAT, WLZEFF_IPL_TYPE_INT, WLZEFF_IPL_TYPE_SHORT, WLZEFF_IPL_TYPE_U_16, WLZEFF_IPL_TYPE_UBYTE, WlzFreeObj(), and WlzFromArray3D().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjIPL	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the '.ipl' file format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

Referenced by WlzEffWriteObj().

static WlzErrorNum WlzEffHeadWriteIPL	(	WlzEffIPLHeader *	header,
		FILE *	fP
	)

Writes an IPL header to the given file stream.

Returns: Woolz error code.

Todo:: Just a stub, still to be written.

Parameters

header	Given header data structure to be written.
fP	Given output file stream.

References WLZ_ERR_UNIMPLEMENTED.

Referenced by WlzEffWriteObjIPL().

WlzObject* WlzEffReadObjJpeg	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a jpeg image frm the given file stream and returns a Woolz object.

Returns: Woolz object read from jpeg image.

Parameters

fP	Given file stream.
dstErr	Destination error pointer, may be NULL.

References ALC_ER_NONE, AlcCalloc(), AlcFree(), AlcFreeStackPush(), _WlzRectValues::freeptr, _WlzGreyP::inp, _WlzGreyV::inv, my_error_exit(), my_error_mgr::pub, _WlzValues::r, _WlzGreyP::rgbp, my_error_mgr::setjmp_buffer, _WlzGreyP::shp, _WlzGreyV::shv, _WlzPixelV::type, _WlzGreyP::ubp, _WlzGreyV::ubv, _WlzPixelV::v, _WlzObject::values, WLZ_ERR_FILE_FORMAT, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_ERR_UNIMPLEMENTED, WLZ_GREY_RGBA, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZ_RGBA_RGBA_SET, WlzFreeObj(), and WlzMakeRect().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjJpeg	(	FILE *	fP,
		WlzObject *	obj,
		char *	params
	)

Writes the given object to a jpeg image.

Returns: Woolz error code.

Parameters

fP	Given file stream.
obj	Given object to be written.
params	Jpeg parameters string, currently this is a single ascii integer, which should have the range 1 - 100 and rpresents the image quality with 100 being lossless.

References _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzDomain::i, _WlzIntervalDomain::kol1, _WlzIntervalDomain::lastkl, _WlzIntervalDomain::lastln, _WlzIntervalDomain::line1, my_error_exit(), _WlzValues::obj, my_error_mgr::pub, _WlzGreyP::rgbp, my_error_mgr::setjmp_buffer, _WlzObject::type, _WlzGreyWSpace::u_grintptr, _WlzGreyP::ubp, _WlzObject::values, WLZ_2D_DOMAINOBJ, WLZ_EMPTY_OBJ, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_EOO, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_UNIMPLEMENTED, WLZ_ERR_VALUES_NULL, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_DOUBLE, WLZ_GREY_ERROR, WLZ_GREY_FLOAT, WLZ_GREY_INT, WLZ_GREY_RGBA, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZ_RGBA_BLUE_GET, WLZ_RGBA_GREEN_GET, WLZ_RGBA_RED_GET, WLZ_TRANS_OBJ, WlzCutObjToBox2D(), WlzFreeObj(), WlzGreyTypeFromObj(), WlzInitGreyScan(), WlzNextGreyInterval(), _WlzIBox2::xMax, _WlzIBox2::xMin, _WlzIBox2::yMax, and _WlzIBox2::yMin.

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjMesh	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using Pascal Frey's tetrahedral mesh file format. The file must start with the records:

Returns: Object read from file.

MeshVersionFormatted 1
Dimension 3

Following this a number of keywords followed by a cardinality and then that number of further data fields follow:

Vertices                       np     xi yi zi ri    {i in 1-np}
Edges                          ne     e1i e2i ri     {i in 1-ne}
Triangles                      nt     vij ri         {i in 1-nt},{j in 1-3}
Quadrilaterals                 nq     vij ri         {i in 1-nq},{j in 1-4}
Tetrahedra                     ntet   vij ri         {i in 1-ntet},{j in 1-4}
Hexaedra                       nh     vij ri         {i in 1-nh},{j in 1-8}
Corners                        nc     vi             {i in 1-nc}
RequiredVertices               nrv    vi             {i in 1-nrv}
Ridges                         nr     ei             {i in 1-nr}
RequiredEdges                  nre    vi             {i in 1-nre}
Normals                        nn     xi yi zi       {i in 1-nn}
Tangents                       nnt    xi yi zi       {i in 1-nnt}
NormalAtVertices               nv     vi ni          {i in 1-nv}
NormalAtTriangleVertices       ntv    ti vj ni       {i in 1-ntv}
NormalAtQuadrilateralVertices  nqv    qi vj ni       {i in 1-nqv}
TangentAtEdges                 te     ei vj ni       {i in 1-te}

At any point outside of a data field a comment character ('#') indicates that the rest of the line is to be ignored. The file terminates with the keyword: End.

Only tetrahedral meshes can be read by this function and all fields except for the start, Vertices and Tetrahedra fields are ignored.

The resulting object will be of type WLZ_CMESH_3D.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References AlcMalloc(), AlcVectorExtendAndGet(), AlcVectorItemGet(), _WlzCMesh3D::bBox, _WlzDomain::cm3, _WlzValues::core, _WlzDomain::core, _WlzCMeshRes::elm, _WlzCMeshNod3D::flags, _WlzCMeshElm3D::flags, _WlzCMeshRes::nod, _WlzCMesh3D::res, _WlzCMeshEntRes::vec, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_3D, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WlzBoundingBoxVtx3D(), WlzCMeshFree3D(), WlzCMeshNew3D(), WlzCMeshNewElm3D(), WlzCMeshNewNod3D(), WlzCMeshReassignGridCells3D(), WlzCMeshUpdateMaxSqEdgLen3D(), and WlzMakeMain().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjMesh	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using Pascal Frey's tetrahedral mesh file format. See WlzEffReadObjMesh() for details of the format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcFree(), AlcMalloc(), AlcVectorItemGet(), _WlzDomain::cm3, _WlzDomain::core, _WlzObject::domain, _WlzCMeshRes::elm, _WlzCMeshNod3D::idx, _WlzCMeshElm3D::idx, _WlzCMeshEntRes::maxEnt, _WlzCMeshRes::nod, _WlzCMeshEntRes::numEnt, _WlzCMeshNod3D::pos, _WlzCMesh3D::res, _WlzObject::type, _WlzCMesh3D::type, _WlzCMeshEntRes::vec, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_3D, WLZ_CMESH_ELM3D_GET_NODE_0, WLZ_CMESH_ELM3D_GET_NODE_1, WLZ_CMESH_ELM3D_GET_NODE_2, WLZ_CMESH_ELM3D_GET_NODE_3, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, and WLZ_ERR_WRITE_INCOMPLETE.

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjNifti	(	const char *	gvnFileName,
		int	sTrans,
		int	gTrans,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the NIfTI format. In some cases (for example when the NIfTI object has complex values) a compound object may be returned. A text property is created for the returned object, containing various fields of the NIfTI header, some of which may not be used in the conversion. The qform transform/quaternion, mapping the image to it's source (scanner) coordinates is copied text property but no transform is either created of applied for it. The sform transform/quaternion is always applied if the parameter flag is set, otherwise it ionly is applied if it is a pure translation. If the sform transform is not applied then it will (if not an identity transform) be used to create a trans-obj. If affine transforms are applied then WLZ_INTERPOLATION_NEAREST is used. NIfTI allows the linear transformation of grey values. This will only be applied if the parameter flag is set. The grey scaling will result in floating point image grey values.

Returns: New Woolz object or NULL on error.

Parameters

gvnFileName	Given file name.
sTrans	If non-zero the NIfTI spatial transform is used to build a WLZ_TRANS_OBJ, otherwise any shift is applied but the remaining transform components are ignored.
gTrans	Apply the NIfTI grey scaling if non-zero.
dstErr	Destination error code, may be NULL.

References ALC_ER_NONE, AlcDLPListEntryAppend(), AlcFree(), _WlzProperty::core, _WlzGreyV::flv, _WlzPropertyList::list, _WlzAffineTransform::mat, _WlzProperty::name, _WlzValues::obj, _WlzObject::plist, _WlzDomain::t, _WlzProperty::text, _WlzPixelV::type, _WlzObject::type, _WlzPixelV::v, _WlzIVertex3::vtX, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_2D_DOMAINOBJ, WLZ_3D_DOMAINOBJ, WLZ_COMPOUND_ARR_1, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_UNIMPLEMENTED, WLZ_GREY_FLOAT, WLZ_TRANS_OBJ, WLZ_TRANSFORM_2D_AFFINE, WLZ_TRANSFORM_2D_TRANS, WLZ_TRANSFORM_3D_AFFINE, WLZ_TRANSFORM_3D_TRANS, WLZ_TRANSFORM_EMPTY, WlzAssignObject(), WlzAssignPropertyList(), WlzFreeAffineTransform(), WlzFreeObj(), WlzFreeProperty(), WlzFreePropertyList(), WlzFreePropertyListEntry(), WlzMakeAffineTransform(), WlzMakeMain(), WlzMakeNameProperty(), WlzMakePropertyList(), WlzMakeTextProperty(), WlzScalarMulAdd(), and WlzShiftObject().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjNifti	(	const char *	gvnFileName,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file(s) using the NIfTI file format.

Returns: Woolz error code.

Parameters

gvnFileName	Given file name with .hdr, .img or no extension.
obj	Given woolz object.

References Alc2Free(), Alc3Free(), AlcCalloc(), AlcFree(), AlcMalloc(), _WlzValues::core, _WlzDomain::core, _WlzGreyP::dbp, _WlzObject::domain, _WlzGreyP::flp, _WlzDomain::i, _WlzGreyP::inp, _WlzGreyV::inv, _WlzIntervalDomain::kol1, _WlzPlaneDomain::kol1, _WlzIntervalDomain::lastkl, _WlzPlaneDomain::lastkl, _WlzIntervalDomain::lastln, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzIntervalDomain::line1, _WlzPlaneDomain::line1, _WlzGreyP::lnp, _WlzCompoundArray::o, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzValues::r, _WlzGreyP::rgbp, _WlzGreyP::shp, _WlzPixelV::type, _WlzObject::type, _WlzGreyP::ubp, _WlzGreyP::v, _WlzPixelV::v, _WlzObject::values, _WlzRectValues::values, _WlzVoxelValues::values, _WlzValues::vox, _WlzPlaneDomain::voxel_size, _WlzIVertex2::vtX, _WlzIVertex3::vtX, _WlzIVertex2::vtY, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_2D_DOMAINOBJ, WLZ_3D_DOMAINOBJ, WLZ_CLAMP, WLZ_COMPOUND_ARR_1, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_GREY_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_UNIMPLEMENTED, WLZ_ERR_VALUES_NULL, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_DOUBLE, WLZ_GREY_FLOAT, WLZ_GREY_INT, WLZ_GREY_LONG, WLZ_GREY_RGBA, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZ_RGBA_ALPHA_SET, WLZ_RGBA_BLUE_SET, WLZ_RGBA_GREEN_SET, WLZ_RGBA_RED_SET, WlzAssignObject(), WlzFreeObj(), WlzGreySize(), WlzGreyTypeFromObj(), WlzMakeCompoundArray(), WlzMakeCuboid(), WlzMakeRect(), WlzToArray2D(), WlzToArray3D(), WlzValueConvertPixel(), WlzValueCopyDoubleToDouble(), WlzValueCopyFloatToFloat(), WlzValueCopyIntToInt(), WlzValueCopyRGBAToRGBA(), WlzValueCopyShortToShort(), WlzValueCopyUByteToUByte(), _WlzIBox2::xMax, _WlzIBox3::xMax, _WlzIBox2::xMin, _WlzIBox3::xMin, _WlzIBox2::yMax, _WlzIBox3::yMax, _WlzIBox2::yMin, _WlzIBox3::yMin, _WlzIBox3::zMax, and _WlzIBox3::zMin.

Referenced by WlzEffWriteObj().

WlzErrorNum WlzEffNodeEleFileNames	(	char **	fileBody,
		char **	nodeFileName,
		char **	eleFileName,
		const char *	gvnFileName
	)

Builds the node/ele file names from the given file name. These strings should be free'd using AlcFree() when no longer required.

Returns: Woolz error number.

Parameters

fileBody	Dest ptr for the file body.
nodeFileName	Dest ptr for the '.node' file name.
eleFileName	Dest ptr for the '.ele' file name.
gvnFileName	Given file name with .node or no extension.

References AlcMalloc(), WLZ_ERR_MEM_ALLOC, and WLZ_ERR_NONE.

Referenced by WlzEffReadObjNodeEle(), and WlzEffWriteObjNodeEle().

WlzObject* WlzEffReadObjNodeEle	(	const char *	gvnFileName,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from a pair of files using the node/ele format. The given file name is used to generate the '.node' and '.ele' filenames.

Returns: Object read from file.

Parameters

gvnFileName	Given file name.
dstErr	Destination error number ptr, may be NULL.

References AlcFree(), AlcMalloc(), AlcVectorExtendAndGet(), AlcVectorItemGet(), _WlzCMesh2D::bBox, _WlzCMesh3D::bBox, _WlzDomain::cm2, _WlzDomain::cm3, _WlzValues::core, _WlzDomain::core, _WlzVertexP::d2, _WlzVertexP::d3, _WlzCMeshRes::elm, _WlzCMeshNod2D::flags, _WlzCMeshNod3D::flags, _WlzCMeshP::m2, _WlzCMeshP::m3, _WlzCMeshRes::nod, _WlzCMeshNod2D::pos, _WlzCMeshNod3D::pos, _WlzCMesh2D::res, _WlzCMesh3D::res, _WlzVertexP::v, _WlzCMeshP::v, _WlzCMeshEntRes::vec, _WlzDVertex2::vtX, _WlzDVertex3::vtX, _WlzDVertex2::vtY, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_2D, WLZ_CMESH_3D, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_READ_INCOMPLETE, WlzCMeshFree2D(), WlzCMeshFree3D(), WlzCMeshNew2D(), WlzCMeshNew3D(), WlzCMeshNewElm2D(), WlzCMeshNewElm3D(), WlzCMeshNewNod2D(), WlzCMeshNewNod3D(), WlzCMeshReassignGridCells2D(), WlzCMeshReassignGridCells3D(), WlzCMeshUpdateMaxSqEdgLen2D(), WlzCMeshUpdateMaxSqEdgLen3D(), WlzEffNodeEleFileNames(), WlzMakeMain(), _WlzDBox2::xMax, _WlzDBox3::xMax, _WlzDBox2::xMin, _WlzDBox3::xMin, _WlzDBox2::yMax, _WlzDBox3::yMax, _WlzDBox2::yMin, _WlzDBox3::yMin, _WlzDBox3::zMax, and _WlzDBox3::zMin.

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjNodeEle	(	const char *	gvnFileName,
		WlzObject *	obj
	)

Writes the given Woolz object to a pair of files using the node/ele two part mesh file format. The given file name is used to generate the '.node' and '.ele' filenames.

Returns: Woolz error number.

Parameters

gvnFileName	Given file name with '.node' or no extension.
obj	Given woolz object.

References AlcFree(), AlcMalloc(), AlcVectorItemGet(), _WlzDomain::cm2, _WlzDomain::cm3, _WlzDomain::core, _WlzObject::domain, _WlzCMeshRes::elm, _WlzCMeshElm2D::idx, _WlzCMeshElm3D::idx, _WlzCMeshP::m2, _WlzCMeshP::m3, _WlzCMeshEntRes::maxEnt, _WlzCMeshRes::nod, _WlzCMeshEntRes::numEnt, _WlzCMeshNod2D::pos, _WlzCMeshNod3D::pos, _WlzCMesh2D::res, _WlzCMesh3D::res, _WlzObject::type, _WlzCMesh2D::type, _WlzCMesh3D::type, _WlzCMeshP::v, _WlzCMeshEntRes::vec, _WlzDVertex2::vtY, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_2D, WLZ_CMESH_3D, WLZ_CMESH_ELM2D_GET_NODE_0, WLZ_CMESH_ELM2D_GET_NODE_1, WLZ_CMESH_ELM2D_GET_NODE_2, WLZ_CMESH_ELM3D_GET_NODE_0, WLZ_CMESH_ELM3D_GET_NODE_1, WLZ_CMESH_ELM3D_GET_NODE_2, WLZ_CMESH_ELM3D_GET_NODE_3, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_WRITE_INCOMPLETE, and WlzEffNodeEleFileNames().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjNrrd	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the NRRD file format. Not all NRRD files and not all encodings have been implemented. This function will currently only read pixel/voxel data, where this data is either raw or encoded using bzip2 or gzip compression. Use of these compression methods depends on their availability at compile time. If the input NRRD pixel/voxel type is either signed char or unsigned short then it is promoted to either signed short or signed int in the output Woolz object. Unused NRRD header fields are encoded as a text property of the output object.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References AlcFree(), _WlzEffNrrdHeader::centering, _WlzEffNrrdHeader::centers, _WlzEffNrrdHeader::dimension, _WlzEffNrrdHeader::kinds, _WlzEffNrrdHeader::labels, _WlzEffNrrdHeader::space, _WlzEffNrrdHeader::spaceDirections, _WlzEffNrrdHeader::spaceUnits, _WlzEffNrrdHeader::thickness, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, and WLZ_ERR_READ_INCOMPLETE.

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjNrrd	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the NRRD file format. This function will currently only write 2 or 3D domain objects. If the object has no values then unsigned byte values are written with background = 0 and forground = 255. If gzip compression is available at compile time the output file uses gzip compression, otherwise raw data are output.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjObj	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the Wavefront OBJ file format. This format consists of the following possible fields (one per line): Vertex data -v vertex geometry -vt ignored -vn vertex normal -vp ignored -cstype ignored -deg ignored -bmat ignored -step ignored Elements -p ignored -l ignored -f face -curv ignored -curv2 ignored -surf ignored Freeform elements -param ignored -trim ignored -hole ignored -scrv ignored -sp ignored -end ignored Freeform surface connectivity -con ignored Grouping -g ignored -o ignored -s ignored -mg ignored Rendering attributes -bevel ignored -c_interp ignored -d_interp ignored -lod ignored -usemtl ignored -mtllib ignored -shadow_obj ignored -trace_obj ignored -ctech ignored -stech ignored Comments

ignored Only triangulated surface models can be read. All groupings will be amalgamated into one.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References ALC_STRTOK_R, AlcVectorExtendAndGet(), AlcVectorFree(), AlcVectorItemGet(), AlcVectorNew(), _WlzValues::core, _WlzDomain::core, _WlzDomain::ctr, _WlzContour::model, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CONTOUR, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_GMMOD_3D, WLZ_GMMOD_3N, WlzAssignGMModel(), WlzFreeContour(), WlzFreeObj(), WlzGMModelConstructSimplex3D(), WlzGMModelConstructSimplex3N(), WlzGMModelFree(), WlzGMModelNew(), WlzMakeContour(), and WlzMakeMain().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjObj	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file stream using the Wavefront OBJ file format, see WlzEffReadObjObj().

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcFree(), AlcMalloc(), AlcVectorItemGet(), _WlzDomain::cm2d5, _WlzDomain::core, _WlzDomain::ctr, _WlzGMVertexT::diskT, _WlzObject::domain, _WlzGMLoopT::edgeT, _WlzCMeshRes::elm, _WlzGMModelR::face, _WlzGMVertex::idx, _WlzGMFace::idx, _WlzCMeshNod2D5::idx, _WlzCMeshElm2D5::idx, _WlzGMResIdx::idxCnt, _WlzGMResIdx::idxLut, _WlzGMFace::loopT, _WlzCMeshEntRes::maxEnt, _WlzContour::model, _WlzGMEdgeT::next, _WlzCMeshRes::nod, _WlzGMResource::numElm, _WlzGMResource::numIdx, _WlzCMeshNod2D5::pos, _WlzGMEdgeT::prev, _WlzGMModel::res, _WlzCMesh2D5::res, _WlzGMModel::type, _WlzObject::type, _WlzCMesh2D5::type, _WlzGMResource::vec, _WlzCMeshEntRes::vec, _WlzGMDiskT::vertex, _WlzGMModelR::vertex, _WlzGMResIdxTb::vertex, _WlzGMEdgeT::vertexT, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_2D5, WLZ_CONTOUR, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GMELMFLG_VERTEX, WLZ_GMMOD_3D, WLZ_GMMOD_3I, WLZ_GMMOD_3N, WlzCMeshElmGetNodes2D5(), WlzGMModelResIdx(), WlzGMModelResIdxFree(), WlzGMVertexGetG3D(), and WlzGMVertexGetG3N().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjPic	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the BioRad Confocal '.pic' format.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References Alc3Free(), ALC_ER_NONE, AlcShort3Malloc(), AlcUnchar3Malloc(), _WlzObject::domain, _WlzDomain::p, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_READ_INCOMPLETE, WLZ_GREY_ERROR, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZEFF_PIC_HEAD_WORD_GET, WLZEFF_PIC_HEADBYTES, WLZEFF_PIC_MAGIC, WLZEFF_PIC_OFF_BYTEPIX, WLZEFF_PIC_OFF_MAGIC, WLZEFF_PIC_OFF_NPIC, WLZEFF_PIC_OFF_NX, WLZEFF_PIC_OFF_NY, and WlzFromArray3D().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjPic	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the BioRad Confocal '.pic' format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcUnchar3Free(), _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzPlaneDomain::kol1, _WlzPlaneDomain::lastkl, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzPlaneDomain::line1, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzObject::values, _WlzIVertex3::vtX, _WlzIVertex3::vtY, _WlzIVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_UBYTE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, WLZEFF_PIC_HEAD_WORD_SET, WLZEFF_PIC_HEADBYTES, WLZEFF_PIC_MAGIC, WLZEFF_PIC_OFF_BLACKVAL, WLZEFF_PIC_OFF_BYTEPIX, WLZEFF_PIC_OFF_MAGIC, WLZEFF_PIC_OFF_MERGED, WLZEFF_PIC_OFF_NPIC, WLZEFF_PIC_OFF_NX, WLZEFF_PIC_OFF_NY, WLZEFF_PIC_OFF_RGB, WLZEFF_PIC_OFF_WHITEVAL, and WlzToArray3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjPly2	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the Riken PLY2 triangular mesh file format. This format simply consists of:

Returns: Object read from file.

              <n vertices (int)>
              <n triangles (int)>
              <vertex (double double double)>
              ...
              <triangle (int int int)>
              ...

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References AlcFree(), AlcMalloc(), _WlzValues::core, _WlzDomain::core, _WlzDomain::ctr, _WlzContour::model, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CONTOUR, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_GMMOD_3D, WlzAssignGMModel(), WlzFreeContour(), WlzFreeObj(), WlzGMModelConstructSimplex3D(), WlzGMModelFree(), WlzGMModelNew(), WlzMakeContour(), and WlzMakeMain().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjPly2	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file stream using the Riken PLY2 triangular mesh file format, see WlzEffReadObjPly2().

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcFree(), AlcMalloc(), AlcVectorItemGet(), _WlzDomain::cm2d5, _WlzDomain::core, _WlzDomain::ctr, _WlzGMVertexT::diskT, _WlzObject::domain, _WlzGMLoopT::edgeT, _WlzCMeshRes::elm, _WlzGMModelR::face, _WlzGMVertex::idx, _WlzGMFace::idx, _WlzCMeshNod2D5::idx, _WlzCMeshElm2D5::idx, _WlzGMResIdx::idxCnt, _WlzGMResIdx::idxLut, _WlzGMFace::loopT, _WlzCMeshEntRes::maxEnt, _WlzContour::model, _WlzGMEdgeT::next, _WlzCMeshRes::nod, _WlzGMResource::numElm, _WlzCMeshEntRes::numEnt, _WlzGMResource::numIdx, _WlzCMeshNod2D5::pos, _WlzGMEdgeT::prev, _WlzGMModel::res, _WlzCMesh2D5::res, _WlzGMModel::type, _WlzObject::type, _WlzCMesh2D5::type, _WlzGMResource::vec, _WlzCMeshEntRes::vec, _WlzGMDiskT::vertex, _WlzGMModelR::vertex, _WlzGMResIdxTb::vertex, _WlzGMEdgeT::vertexT, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_2D5, WLZ_CONTOUR, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GMELMFLG_VERTEX, WLZ_GMMOD_3D, WLZ_GMMOD_3I, WLZ_GMMOD_3N, WlzCMeshElmGetNodes2D5(), WlzGMModelResIdx(), WlzGMModelResIdxFree(), and WlzGMVertexGetG3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjPnm	(	const char *	gvnFileName,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given file(s) using the '.pnm' file format.

Returns: Object read from file.

Parameters

gvnFileName	Given file name.
dstErr	Destination error number ptr, may be NULL.

References WLZ_ERR_NONE, WLZEFF_FORMAT_PNM, and WlzEffReadObjStack().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjPnm	(	const char *	gvnFileName,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file(s) using the '.pnm' file format.

Returns: Woolz error number.

Parameters

gvnFileName	Given file name.
obj	Destination error number ptr, may be NULL.

References WLZ_ERR_NONE, WLZEFF_FORMAT_PNM, and WlzEffWriteObjStack().

Referenced by WlzEffWriteObj().

WlzErrorNum WlzEffWriteObjPnm2D	(	const char *	fNameStr,
		WlzObject *	obj,
		WlzIVertex2	imgSz,
		WlzIVertex2	imgOrg,
		unsigned char *	data,
		unsigned char	bgd
	)

Writes the given 2D Woolz object to the given file using the '.pnm' file format.

Returns: Woolz error number.

Parameters

fNameStr	Given file name.
obj	Given woolz object.
imgSz	Required image size.
imgOrg	Required image origin.
data	Buffer of imgSz bytes.
bgd	Background value.

References AlcFree(), _WlzValues::core, _WlzRectValues::freeptr, _WlzGreyP::inp, _WlzValues::r, _WlzObject::type, _WlzObject::values, _WlzRectValues::values, _WlzIVertex2::vtX, _WlzIVertex2::vtY, WLZ_2D_DOMAINOBJ, WLZ_ERR_NONE, WLZ_ERR_READ_EOF, WLZ_ERR_WRITE_EOF, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_UBYTE, WlzCutObjToValBox2D(), WLZEFF_PGM_MAGIC, WlzFreeObj(), _WlzIBox2::xMax, _WlzIBox2::xMin, _WlzIBox2::yMax, and _WlzIBox2::yMin.

Referenced by WlzEffWriteObjStack().

WlzErrorNum WlzEffReadObjPnmData2D	(	FILE *	fP,
		WlzIVertex2 *	gvnImgSz,
		unsigned char ***	data
	)

Reads the data from a pgm file into the data array given.

Returns: Woolz error number.

Parameters

fP	Given file stream.
gvnImgSz	Dst ptr for image size which is assumed valid if height and width are non zero.
data	Ptr to 2D array for data.

References ALC_ER_NONE, AlcUnchar2Malloc(), _WlzIVertex2::vtX, _WlzIVertex2::vtY, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_READ_INCOMPLETE, and WLZEFF_PGM_MAGIC.

Referenced by WlzEffWriteObjStack().

WlzObject* WlzEffReadObjPvl	(	const char *	gvnFileName,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from Drishti pvl.nc files.

Returns: Object read from file.

Parameters

gvnFileName	Given file name.
dstErr	Destination error number ptr, may be NULL.

References WLZ_ERR_UNIMPLEMENTED.

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjPvl	(	const char *	gvnFileName,
		WlzObject *	obj
	)

Writes the given Woolz object to a pair of files using the Derishti .pvl.nc file format.

Returns: Woolz error number.

Parameters

gvnFileName	Given file name with .ics, .ids or no extension.
obj	Given woolz object.

References AlcFree(), AlcUnchar3Free(), _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzGreyP::inp, _WlzPlaneDomain::kol1, _WlzPlaneDomain::lastkl, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzPlaneDomain::line1, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzGreyP::v, _WlzObject::values, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzDVertex3::vtX, _WlzIVertex3::vtY, _WlzDVertex3::vtY, _WlzIVertex3::vtZ, _WlzDVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_EOF, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_UBYTE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, and WlzToArray3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzExtFFReadObjRaw	(	FILE *	fp,
		int	numKols,
		int	numLines,
		int	numPlanes,
		int	bytesPerPixel,
		int	bitsPerChannel,
		int	numChannels,
		int	byteOrder,
		WlzErrorNum *	dstErr
	)

Reads a raw 'brick of bytes' object into a Woolz object.

Returns: Woolz error code.

Parameters

fp	Given file stream.
numKols	Number of columns, x size.
numLines	Number of lines, y size.
numPlanes	Number of planes, z size.
bytesPerPixel	Number of bytes per pixel.
bitsPerChannel	Number of bits per channel.
numChannels	Number of channels.
byteOrder	Byte order.
dstErr	Destination pointer for error code, may be NULL.

References AlcFree(), AlcMalloc(), WLZ_2D_DOMAINOBJ, WLZ_3D_DOMAINOBJ, WLZ_COMPOUND_ARR_1, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_DATA, WLZ_ERR_READ_INCOMPLETE, WLZ_GREY_INT, WLZ_GREY_RGBA, WLZ_GREY_SHORT, and WLZ_GREY_UBYTE.

WlzObject* WlzEffReadObjSlc	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the '.slc' file format.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References Alc3Free(), ALC_ER_NONE, AlcFree(), AlcMalloc(), AlcRealloc(), AlcUnchar3Malloc(), _WlzEffSlcHeader::compression, _WlzObject::domain, _WlzEffSlcHeader::icon, _WlzDomain::p, _WlzEffSlcHeader::size, _WlzEffSlcHeader::spacing, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzFVertex3::vtX, _WlzIVertex3::vtY, _WlzFVertex3::vtY, _WlzIVertex3::vtZ, _WlzFVertex3::vtZ, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_GREY_UBYTE, WlzFreeObj(), and WlzFromArray3D().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjSlc	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the '.slc' file format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References Alc3Free(), AlcFree(), AlcMalloc(), AlcRealloc(), _WlzEffSlcHeader::bits, _WlzEffSlcHeader::compression, _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzEffSlcHeader::icon, _WlzEffSlcHeader::iconSize, _WlzPlaneDomain::kol1, _WlzPlaneDomain::lastkl, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzPlaneDomain::line1, _WlzEffSlcHeader::magic, _WlzEffSlcHeader::modification, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzEffSlcHeader::size, _WlzEffSlcHeader::source, _WlzEffSlcHeader::spacing, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzEffSlcHeader::units, _WlzObject::values, _WlzPlaneDomain::voxel_size, _WlzIVertex2::vtX, _WlzDVertex2::vtX, _WlzIVertex3::vtX, _WlzFVertex3::vtX, _WlzIVertex2::vtY, _WlzDVertex2::vtY, _WlzIVertex3::vtY, _WlzFVertex3::vtY, _WlzIVertex3::vtZ, _WlzFVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_READ_INCOMPLETE, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_EOF, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_UBYTE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, WLZEFF_SLC_DATAMOD_OTHER, WLZEFF_SLC_DATASRC_OTHER, WLZEFF_SLC_DATAUNITS_MICROMETER, WLZEFF_SLC_MAGIC, and WlzToArray3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjSMesh	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the GRUMMP smesh file format. This format is:

Returns: Object read from file.

  # comment for rest of record
  <n nodes> <dim (always 3)> <n attrib> <n boundary markers>
  <node idx> <x> <y> <z> [<attributes>] [<boundary mark>]
  ...
  <n facets> <n boundary markers>
  <n nodes> <node idx> <node idx> <node idx> <facet idx> [<boundary mark>]
  ...
  <n holes>
  <hole idx> <x> <y> <z>
  ...
  <n region>
  <region idx> <x> <y> <z> <region n> <region attributes>
  ...

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References AlcFree(), AlcMalloc(), _WlzValues::core, _WlzDomain::core, _WlzDomain::ctr, _WlzContour::model, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CONTOUR, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_GMMOD_3D, WlzAssignGMModel(), WlzFreeContour(), WlzFreeObj(), WlzGMModelConstructSimplex3D(), WlzGMModelFree(), WlzGMModelNew(), WlzMakeContour(), and WlzMakeMain().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjSMesh	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file stream using the GRUMMP smesh file format, see WlzEffReadObjSMesh().

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcFree(), AlcMalloc(), AlcVectorItemGet(), _WlzDomain::cm2d5, _WlzDomain::core, _WlzDomain::ctr, _WlzGMVertexT::diskT, _WlzObject::domain, _WlzGMLoopT::edgeT, _WlzCMeshRes::elm, _WlzGMModelR::face, _WlzGMVertex::idx, _WlzGMFace::idx, _WlzCMeshNod2D5::idx, _WlzCMeshElm2D5::idx, _WlzGMResIdx::idxCnt, _WlzGMResIdx::idxLut, _WlzGMFace::loopT, _WlzCMeshEntRes::maxEnt, _WlzContour::model, _WlzGMEdgeT::next, _WlzCMeshRes::nod, _WlzGMResource::numElm, _WlzCMeshEntRes::numEnt, _WlzGMResource::numIdx, _WlzCMeshNod2D5::pos, _WlzGMEdgeT::prev, _WlzGMModel::res, _WlzCMesh2D5::res, _WlzGMModel::type, _WlzObject::type, _WlzCMesh2D5::type, _WlzGMResource::vec, _WlzCMeshEntRes::vec, _WlzGMDiskT::vertex, _WlzGMModelR::vertex, _WlzGMResIdxTb::vertex, _WlzGMEdgeT::vertexT, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_2D5, WLZ_CONTOUR, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GMELMFLG_VERTEX, WLZ_GMMOD_3D, WLZ_GMMOD_3I, WLZ_GMMOD_3N, WlzCMeshElmGetNodes2D5(), WlzGMModelResIdx(), WlzGMModelResIdxFree(), and WlzGMVertexGetG3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjStack	(	const char *	gvnFileName,
		WlzEffFormat	fFmt,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given file(s) using the given (2D) file format.

Returns: Object read from file.

Parameters

gvnFileName	Given file name.
fFmt	Given file format (must be a 2D file format).
dstErr	Destination error number ptr, may be NULL.

References WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, and WLZ_ERR_READ_EOF.

Referenced by WlzEffReadObjBmp(), and WlzEffReadObjPnm().

WlzErrorNum WlzEffWriteObjStack	(	const char *	gvnFileName,
		WlzEffFormat	fFmt,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file(s) using the given (2D) file format.

Returns: Woolz error number.

Parameters

gvnFileName	Given file name.
fFmt	Given file format (must be a 2D file format).
obj	Given woolz object.

References Alc2Free(), Alc3Free(), ALC_ER_NONE, AlcFree(), AlcMalloc(), AlcUnchar3Malloc(), _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzPlaneDomain::domains, _WlzDomain::i, _WlzIntervalDomain::kol1, _WlzPlaneDomain::kol1, _WlzIntervalDomain::lastkl, _WlzPlaneDomain::lastkl, _WlzIntervalDomain::lastln, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzIntervalDomain::line1, _WlzPlaneDomain::line1, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzGreyV::ubv, _WlzPixelV::v, _WlzObject::values, _WlzVoxelValues::values, _WlzEffStackCtrHeader::volOrigin, _WlzEffStackCtrHeader::volSize, _WlzValues::vox, _WlzPlaneDomain::voxel_size, _WlzEffStackCtrHeader::voxSize, _WlzIVertex2::vtX, _WlzIVertex3::vtX, _WlzFVertex3::vtX, _WlzIVertex2::vtY, _WlzIVertex3::vtY, _WlzFVertex3::vtY, _WlzIVertex3::vtZ, _WlzFVertex3::vtZ, WLZ_2D_DOMAINOBJ, WLZ_3D_DOMAINOBJ, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_DATA, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_READ_INCOMPLETE, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_EOF, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_UBYTE, WLZ_INTERVALDOMAIN_INTVL, WLZ_INTERVALDOMAIN_RECT, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, WlzAssignObject(), WLZEFF_FORMAT_BMP, WLZEFF_FORMAT_PNM, WLZEFF_STACK_CTR_COMMENT, WLZEFF_STACK_CTR_FIELDSEP, WLZEFF_STACK_CTR_FILES, WLZEFF_STACK_CTR_IDENT, WLZEFF_STACK_CTR_IDENTSTR, WLZEFF_STACK_CTR_IDENTVERSION, WLZEFF_STACK_CTR_RECORDMAX, WLZEFF_STACK_CTR_VOLORIGIN, WLZEFF_STACK_CTR_VOLSIZE, WLZEFF_STACK_CTR_VOXSIZE, WLZEFF_STACK_NAMEDIGITS, WlzEffReadObjBmpData2D(), WlzEffReadObjPnmData2D(), WlzEffWriteObjBmp2D(), WlzEffWriteObjPnm2D(), WlzFreeObj(), WlzFromArray2D(), WlzFromArray3D(), WlzGetBackground(), WlzMakeMain(), and WlzValueConvertPixel().

Referenced by WlzEffWriteObjBmp(), and WlzEffWriteObjPnm().

WlzObject* WlzEffReadObjStl	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the stereolithography stl surface file format. This format has surface definitions defined by a name and a collection of facet normals and loops. Each facet loop has the cooordinates of it's vertices. Only triangulated surface models can be read and all solids will be treated as one.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References ALC_STRTOK_R, _WlzGreyV::bytes, _WlzValues::core, _WlzDomain::core, _WlzDomain::ctr, _WlzGreyV::flv, _WlzGreyV::inv, _WlzContour::model, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CONTOUR, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZ_GMMOD_3D, WlzAssignGMModel(), WlzFreeContour(), WlzFreeObj(), WlzGMModelConstructSimplex3D(), WlzGMModelFree(), WlzGMModelNew(), WlzMakeContour(), and WlzMakeMain().

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjStl	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file stream using the stereolithography stl file format, see WlzEffReadObjStl().

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcMalloc(), AlcVectorItemGet(), _WlzDomain::cm2d5, _WlzDomain::core, _WlzDomain::ctr, _WlzObject::domain, _WlzCMeshRes::elm, _WlzGMModelR::face, _WlzGMFace::idx, _WlzCMeshElm2D5::idx, _WlzCMeshEntRes::maxEnt, _WlzContour::model, _WlzCMeshRes::nod, _WlzGMResource::numElm, _WlzGMResource::numIdx, _WlzCMeshNod2D5::pos, _WlzGMModel::res, _WlzCMesh2D5::res, _WlzGMModel::type, _WlzObject::type, _WlzCMesh2D5::type, _WlzGMResource::vec, _WlzCMeshEntRes::vec, _WlzGMModelR::vertex, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_2D5, WLZ_CONTOUR, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GMMOD_3D, WLZ_GMMOD_3I, WLZ_GMMOD_3N, WlzCMeshElmGetNodes2D5(), WlzGeomTriangleNormal(), WlzGMFaceGetG3D(), and WlzGMModelResIdxFree().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjTiff	(	const char *	tiffFileName,
		int	split,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given file using the TIFF format.

Returns: Object read from file.

Parameters

tiffFileName	Given file name.
split	If the image is tiled return individual tiles within a compound object.
dstErr	Destination error number ptr, may be NULL.

References AlcFree(), AlcMalloc(), _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzPlaneDomain::domains, _WlzDomain::i, _WlzGreyP::inp, _WlzGreyV::inv, _WlzIntervalDomain::kol1, _WlzIntervalDomain::lastkl, _WlzIntervalDomain::lastln, _WlzIntervalWSpace::linbot, _WlzIntervalDomain::line1, _WlzIntervalWSpace::linpos, _WlzCompoundArray::o, _WlzDomain::p, _WlzGreyP::rgbp, _WlzGreyP::shp, _WlzGreyWSpace::u_grintptr, _WlzGreyP::ubp, _WlzPixelV::v, _WlzObject::values, _WlzVoxelValues::values, _WlzValues::vox, _WlzPlaneDomain::voxel_size, WLZ_2D_DOMAINOBJ, WLZ_3D_DOMAINOBJ, WLZ_COMPOUND_ARR_2, WLZ_ERR_EOO, WLZ_ERR_FILE_FORMAT, WLZ_ERR_GREY_TYPE, WLZ_ERR_IMAGE_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_EOF, WLZ_ERR_READ_INCOMPLETE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_BIT, WLZ_GREY_DOUBLE, WLZ_GREY_FLOAT, WLZ_GREY_INT, WLZ_GREY_LONG, WLZ_GREY_RGBA, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZ_MAX, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, WlzAssignDomain(), WlzAssignObject(), WlzAssignValues(), WlzCutObjToBox2D(), WlzFreeDomain(), WlzFreeObj(), WlzFreeValues(), WlzGetBackground(), WlzGreyRange(), WlzGreyTypeFromObj(), WlzInitGreyScan(), WlzMakeCompoundArray(), WlzMakeMain(), WlzMakePlaneDomain(), WlzMakeVoxelValueTb(), WlzNextGreyInterval(), _WlzIBox2::xMax, _WlzIBox2::xMin, _WlzIBox2::yMax, and _WlzIBox2::yMin.

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjTiff	(	const char *	tiffFileName,
		WlzObject *	obj
	)

Writes the given Woolz object to the given file using the TIFF format.

Returns: Woolz error number.

Parameters

tiffFileName	Given file name with .tif.
obj	Given woolz object.

References _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzPlaneDomain::domains, _WlzPlaneDomain::lastpl, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzObject::type, _WlzPlaneDomain::type, _WlzVoxelValues::type, _WlzObject::values, _WlzVoxelValues::values, _WlzValues::vox, WLZ_2D_DOMAINOBJ, WLZ_3D_DOMAINOBJ, WLZ_COMPOUND_ARR_1, WLZ_COMPOUND_ARR_2, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_FILE_OPEN, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, WlzFreeObj(), WlzGetBackground(), WlzGreySetValue(), and WlzMakeMain().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjVff	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the Sunvision vff (rank 3) file format.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjVff	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the Sunvision vff (rank 3) file format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcUnchar3Free(), _WlzEffVffHeader::aspect, _WlzEffVffHeader::bands, _WlzEffVffHeader::bits, _WlzValues::core, _WlzDomain::core, _WlzObject::domain, _WlzEffVffHeader::extent, _WlzPlaneDomain::kol1, _WlzPlaneDomain::lastkl, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzPlaneDomain::line1, _WlzEffVffHeader::origin, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzEffVffHeader::rank, _WlzEffVffHeader::rawsize, _WlzEffVffHeader::size, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzObject::values, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzDVertex3::vtX, _WlzIVertex3::vtY, _WlzDVertex3::vtY, _WlzIVertex3::vtZ, _WlzDVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_UBYTE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_VOXELVALUETABLE_GREY, and WlzToArray3D().

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjVMesh	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the GRUMMP vmesh tetrahedral mesh file format.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References AlcCalloc(), AlcFree(), AlcMalloc(), AlcVectorExtendAndGet(), AlcVectorItemGet(), _WlzCMesh3D::bBox, _WlzDomain::cm3, _WlzValues::core, _WlzDomain::core, _WlzCMeshRes::elm, _WlzCMeshNod3D::flags, _WlzCMeshRes::nod, _WlzCMeshNod3D::pos, _WlzCMesh3D::res, _WlzCMeshEntRes::vec, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_3D, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WlzCMeshFree3D(), WlzCMeshNew3D(), WlzCMeshNewElm3D(), WlzCMeshNewNod3D(), WlzCMeshReassignGridCells3D(), WlzCMeshUpdateMaxSqEdgLen3D(), WlzMakeMain(), _WlzDBox3::xMax, _WlzDBox3::xMin, _WlzDBox3::yMax, _WlzDBox3::yMin, _WlzDBox3::zMax, and _WlzDBox3::zMin.

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjVMesh	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the GRUMP VMESH tetrahedral mesh file format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcFree(), AlcMalloc(), AlcVectorItemGet(), _WlzDomain::cm3, _WlzDomain::core, _WlzObject::domain, _WlzCMeshFace::edu, _WlzCMeshFace::elm, _WlzCMeshRes::elm, _WlzCMeshElm3D::face, _WlzCMeshNod3D::idx, _WlzCMeshElm3D::idx, _WlzCMeshEntRes::maxEnt, _WlzCMeshEdgU3D::next, _WlzCMeshEdgU3D::nod, _WlzCMeshRes::nod, _WlzCMeshEntRes::numEnt, _WlzCMeshFace::opp, _WlzCMeshNod3D::pos, _WlzCMesh3D::res, _WlzObject::type, _WlzCMesh3D::type, _WlzCMeshEntRes::vec, _WlzDVertex3::vtX, _WlzDVertex3::vtY, _WlzDVertex3::vtZ, WLZ_CMESH_3D, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, and WLZ_ERR_WRITE_INCOMPLETE.

Referenced by WlzEffWriteObj().

WlzObject* WlzEffReadObjVtk	(	FILE *	fP,
		WlzErrorNum *	dstErr
	)

Reads a Woolz object from the given stream using the Visualization Toolkit file format. There is no check on the major and minor version numbers since all files seem compatable.

Returns: Object read from file.

Parameters

fP	Input file stream.
dstErr	Destination error number ptr, may be NULL.

References _WlzEffVtkHeader::type, WLZ_ERR_NONE, WLZ_ERR_PARAM_NULL, WLZ_ERR_READ_INCOMPLETE, WLZEFF_VTK_TYPE_POLYDATA, WLZEFF_VTK_TYPE_RECTILNEAR_GRID, WLZEFF_VTK_TYPE_STRUCTURED_GRID, WLZEFF_VTK_TYPE_STRUCTURED_POINTS, and WLZEFF_VTK_TYPE_UNSTRUCTURED_GRID.

Referenced by WlzEffReadObj().

WlzErrorNum WlzEffWriteObjVtk	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the given Woolz object to the given stream using the Visualization Toolkit file format.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given woolz object.

References AlcFree(), AlcMalloc(), AlcUnchar3Free(), AlcVectorItemGet(), _WlzDomain::cm2, _WlzDomain::cm2d5, _WlzDomain::cm3, _WlzValues::core, _WlzDomain::core, _WlzDomain::ctr, _WlzGMVertexT::diskT, _WlzObject::domain, _WlzGMElemP::edge, _WlzGMModelR::edge, _WlzGMEdge::edgeT, _WlzGMLoopT::edgeT, _WlzCMeshRes::elm, _WlzGMElemP::face, _WlzGMModelR::face, _WlzGMVertex::idx, _WlzGMEdge::idx, _WlzGMFace::idx, _WlzCMeshElm2D::idx, _WlzGMResIdx::idxCnt, _WlzGMResIdx::idxLut, _WlzPlaneDomain::kol1, _WlzPlaneDomain::lastkl, _WlzPlaneDomain::lastln, _WlzPlaneDomain::lastpl, _WlzPlaneDomain::line1, _WlzGMFace::loopT, _WlzCMeshEntRes::maxEnt, _WlzContour::model, _WlzGMEdgeT::next, _WlzCMeshRes::nod, _WlzGMResource::numElm, _WlzCMeshEntRes::numEnt, _WlzGMResource::numIdx, _WlzGMEdgeT::opp, _WlzDomain::p, _WlzPlaneDomain::plane1, _WlzCMeshNod2D::pos, _WlzGMEdgeT::prev, _WlzGMModel::res, _WlzCMesh2D::res, _WlzGMModel::type, _WlzContour::type, _WlzObject::type, _WlzCoreDomain::type, _WlzCoreValues::type, _WlzCMesh2D::type, _WlzObject::values, _WlzGMResource::vec, _WlzCMeshEntRes::vec, _WlzGMElemP::vertex, _WlzGMDiskT::vertex, _WlzGMModelR::vertex, _WlzGMResIdxTb::vertex, _WlzGMEdgeT::vertexT, _WlzPlaneDomain::voxel_size, _WlzIVertex3::vtX, _WlzFVertex3::vtX, _WlzDVertex3::vtX, _WlzDVertex2::vtY, _WlzIVertex3::vtY, _WlzFVertex3::vtY, _WlzDVertex3::vtY, _WlzIVertex3::vtZ, _WlzFVertex3::vtZ, _WlzDVertex3::vtZ, WLZ_3D_DOMAINOBJ, WLZ_CMESH_2D, WLZ_CMESH_2D5, WLZ_CMESH_3D, WLZ_CMESH_ELM2D_GET_NODE_0, WLZ_CMESH_ELM2D_GET_NODE_1, WLZ_CMESH_ELM2D_GET_NODE_2, WLZ_CONTOUR, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_OBJECT_NULL, WLZ_ERR_OBJECT_TYPE, WLZ_ERR_PARAM_NULL, WLZ_ERR_VALUES_NULL, WLZ_ERR_VALUES_TYPE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GMELMFLG_VERTEX, WLZ_GMMOD_2D, WLZ_GMMOD_2I, WLZ_GMMOD_2N, WLZ_GMMOD_3D, WLZ_GMMOD_3I, WLZ_GMMOD_3N, WLZ_GREY_UBYTE, WLZ_PLANEDOMAIN_DOMAIN, WLZ_POINTS, WLZ_VOXELVALUETABLE_GREY, WLZEFF_VTK_VERSION_MAJOR, WLZEFF_VTK_VERSION_MINOR, WlzEffWritePointsVtk(), WlzGMModelResIdx(), WlzGMModelResIdxFree(), WlzGMVertexGetG3D(), WlzGMVertexGetG3N(), and WlzToArray3D().

Referenced by WlzEffWriteObj().

WlzErrorNum WlzEffWritePointsVtk	(	FILE *	fP,
		WlzObject *	obj,
		int	onlyDom
	)

Writes the given Woolz points object to the given stream using the Visualization Toolkit polydata format, but without polygons.

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Given points object.
onlyDom	Only write the points domain if non-zero.

References _WlzVertexP::d2, _WlzVertexP::d3, _WlzObject::domain, _WlzVertexP::i2, _WlzVertexP::i3, _WlzPoints::nPoints, _WlzPoints::points, _WlzValues::pts, _WlzDomain::pts, _WlzPointValues::rank, _WlzPoints::type, _WlzObject::values, _WlzIVertex2::vtX, _WlzDVertex2::vtX, _WlzIVertex3::vtX, _WlzDVertex3::vtX, _WlzIVertex2::vtY, _WlzDVertex2::vtY, _WlzIVertex3::vtY, _WlzDVertex3::vtY, _WlzIVertex3::vtZ, _WlzDVertex3::vtZ, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_NONE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_POINTS_2D, WLZ_POINTS_2I, WLZ_POINTS_3D, WLZ_POINTS_3I, WlzEffWritePointsVtkFieldValues(), and WlzEffWritePointsVtkScalarValues().

Referenced by WlzEffWriteObjVtk().

WlzErrorNum WlzEffWritePointsVtkScalarValues	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the point scalar values of the given object to the given file. It is assumed that the points domain has already been written by WlzEffWritePointsVtk().

Returns: Woolz error number.

Parameters

fP	Output file stream.
obj	Object vith points values for output.

References AlcFree(), _WlzGreyP::dbp, _WlzObject::domain, _WlzGreyP::flp, _WlzGreyP::inp, _WlzNameProperty::name, _WlzPoints::nPoints, _WlzObject::plist, _WlzValues::pts, _WlzDomain::pts, _WlzPointValues::rank, _WlzGreyP::shp, _WlzPoints::type, _WlzGreyP::ubp, _WlzObject::values, _WlzPointValues::values, _WlzPointValues::vType, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_GREY_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GREY_DOUBLE, WLZ_GREY_FLOAT, WLZ_GREY_INT, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZ_POINTS_2D, WLZ_POINTS_2I, WLZ_POINTS_3D, WLZ_POINTS_3I, WlzPropertyListContainsName(), and WlzStringCopyReplace().

Referenced by WlzEffWritePointsVtk().

WlzErrorNum WlzEffWritePointsVtkFieldValues	(	FILE *	fP,
		WlzObject *	obj
	)

Writes the point field values of the given object to the given file. It is assumed that the points domain has already been written by WlzEffWritePointsVtk().

Returns

Woolz error number.

            The VTK file specification does not include an appropriate
            data type for arbitrary dimensional fields so here one is
            defined for point data:

      POINT_DATA <n>
      FIELD <field name> <data type> <rank> [<dim_0>,[...]]

with the following:

n - Number of points.
field name - Non-whitespace ASCII string naming the field.
rank - Rank of the field, 0 for scalar data, 1 for vector data, ....
dim0 - Comma seperated dimensions of the field.

Example for a rank two (3x3) tensor:

      POINT_DATA 2
      FIELD my_tensor float 2 3x3
      1.019 -0.002 0.079  0.003 1.055  0.012 0.002   0.0085 1.019
      1.012 -0.008 0.015 -0.023 1.013 -0.018 7.9e-05 0.0961 1.005

Parameters

fP	Output file stream.
obj	Object vith points values for output.

References AlcFree(), AlcMalloc(), AlcRealloc(), AlcVectorExtendAndGet(), AlcVectorItemGet(), _WlzCMesh2D::bBox, _WlzCMesh3D::bBox, _WlzDomain::cm2, _WlzDomain::cm3, _WlzValues::core, _WlzDomain::core, _WlzDomain::ctr, _WlzVertexP::d3, _WlzEffVtkHeader::dataType, _WlzGreyP::dbp, _WlzPointValues::dim, _WlzObject::domain, _WlzCMeshRes::elm, _WlzCMeshNod2D::flags, _WlzCMeshNod3D::flags, _WlzGreyP::flp, _WlzCMeshElm2D5::idx, _WlzCMeshElm3D::idx, _WlzGreyP::inp, _WlzCMeshP::m2, _WlzCMeshP::m3, _WlzCMeshEntRes::maxEnt, _WlzContour::model, _WlzNameProperty::name, _WlzCMeshRes::nod, _WlzPoints::nPoints, _WlzCMeshEntRes::numEnt, _WlzObject::plist, _WlzCMeshNod2D5::pos, _WlzCMeshNod3D::pos, _WlzValues::pts, _WlzDomain::pts, _WlzPointValues::rank, _WlzCMesh2D::res, _WlzCMesh2D5::res, _WlzCMesh3D::res, _WlzGreyP::shp, _WlzEffVtkHeader::title, _WlzEffVtkHeader::type, _WlzGMModel::type, _WlzPoints::type, _WlzCMesh2D::type, _WlzCMesh2D5::type, _WlzCMesh3D::type, _WlzGreyP::ubp, _WlzCMeshP::v, _WlzObject::values, _WlzPointValues::values, _WlzCMeshEntRes::vec, _WlzEffVtkHeader::versionMajor, _WlzEffVtkHeader::versionMinor, _WlzGMModel::vertexHTSz, _WlzDVertex2::vtX, _WlzDVertex3::vtX, _WlzDVertex2::vtY, _WlzDVertex3::vtY, _WlzPointValues::vType, _WlzDVertex3::vtZ, WLZ_CMESH_2D, WLZ_CMESH_2D5, WLZ_CMESH_3D, WLZ_CMESH_ELM2D5_GET_NODE_0, WLZ_CMESH_ELM2D5_GET_NODE_1, WLZ_CMESH_ELM2D5_GET_NODE_2, WLZ_CMESH_ELM3D_GET_NODE_0, WLZ_CMESH_ELM3D_GET_NODE_1, WLZ_CMESH_ELM3D_GET_NODE_2, WLZ_CMESH_ELM3D_GET_NODE_3, WLZ_CONTOUR, WLZ_ERR_DOMAIN_DATA, WLZ_ERR_DOMAIN_NULL, WLZ_ERR_DOMAIN_TYPE, WLZ_ERR_GREY_TYPE, WLZ_ERR_MEM_ALLOC, WLZ_ERR_NONE, WLZ_ERR_READ_INCOMPLETE, WLZ_ERR_UNIMPLEMENTED, WLZ_ERR_VALUES_DATA, WLZ_ERR_WRITE_INCOMPLETE, WLZ_GMMOD_2D, WLZ_GMMOD_3D, WLZ_GREY_DOUBLE, WLZ_GREY_FLOAT, WLZ_GREY_INT, WLZ_GREY_SHORT, WLZ_GREY_UBYTE, WLZ_NINT, WLZ_POINTS, WLZ_POINTS_2D, WLZ_POINTS_2I, WLZ_POINTS_3D, WLZ_POINTS_3I, WlzAssignGMModel(), WlzCMeshFree2D(), WlzCMeshFree3D(), WlzCMeshNew2D(), WlzCMeshNew3D(), WlzCMeshNewElm2D(), WlzCMeshNewElm3D(), WlzCMeshNewNod2D(), WlzCMeshNewNod3D(), WlzCMeshReassignGridCells2D(), WlzCMeshReassignGridCells3D(), WlzCMeshUpdateMaxSqEdgLen2D(), WlzCMeshUpdateMaxSqEdgLen3D(), WLZEFF_INVALID, WLZEFF_VTK_DATATYPE_ASCII, WLZEFF_VTK_DATATYPE_BINARY, WLZEFF_VTK_POLYDATATYPE_LINES, WLZEFF_VTK_POLYDATATYPE_LOOKUP_TABLE, WLZEFF_VTK_POLYDATATYPE_POINT_DATA, WLZEFF_VTK_POLYDATATYPE_POINTS, WLZEFF_VTK_POLYDATATYPE_POLYGONS, WLZEFF_VTK_POLYDATATYPE_SCALARS, WLZEFF_VTK_POLYDATATYPE_TRIANGLE_STRIPS, WLZEFF_VTK_POLYDATATYPE_VECTORS, WLZEFF_VTK_POLYDATATYPE_VERTICIES, WLZEFF_VTK_TYPE_POLYDATA, WLZEFF_VTK_TYPE_RECTILNEAR_GRID, WLZEFF_VTK_TYPE_STRUCTURED_GRID, WLZEFF_VTK_TYPE_STRUCTURED_POINTS, WLZEFF_VTK_TYPE_UNSTRUCTURED_GRID, WLZEFF_VTK_UNSTRUCTUREDGRIDTYPE_CELL_TYPES, WLZEFF_VTK_UNSTRUCTUREDGRIDTYPE_CELLS, WLZEFF_VTK_UNSTRUCTUREDGRIDTYPE_LOOKUP_TABLE, WLZEFF_VTK_UNSTRUCTUREDGRIDTYPE_POINT_DATA, WLZEFF_VTK_UNSTRUCTUREDGRIDTYPE_POINTS, WLZEFF_VTK_UNSTRUCTUREDGRIDTYPE_SCALARS, WLZEFF_VTK_UNSTRUCTUREDGRIDTYPE_VECTORS, WlzFreeContour(), WlzFreeObj(), WlzGMModelConstructSimplex2D(), WlzGMModelConstructSimplex3D(), WlzGMModelFree(), WlzGMModelNew(), WlzGMModelRehashVHT(), WlzMakeContour(), WlzMakeMain(), WlzMakePoints(), WlzMakePointValues(), WlzPropertyListContainsName(), WlzStringCopyReplace(), WlzStringMatchValue(), _WlzDBox2::xMax, _WlzDBox3::xMax, _WlzDBox2::xMin, _WlzDBox3::xMin, _WlzDBox2::yMax, _WlzDBox3::yMax, _WlzDBox2::yMin, _WlzDBox3::yMin, _WlzDBox3::zMax, and _WlzDBox3::zMin.

Referenced by WlzEffWritePointsVtk().

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Data Structures

Enumerations

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Detailed Description

Enumeration Type Documentation

Function Documentation