nifti1_io
|
Data structures for using the fslio API. Written by Mark Jenkinson, FMRIB. More...
Go to the source code of this file.
Classes | |
struct | FSLIO |
High level data structure for open datasets in the fslio API. More... | |
Defines | |
#define | FSL_TYPE_ANALYZE 0 |
#define | FSL_TYPE_NIFTI 1 |
#define | FSL_TYPE_NIFTI_PAIR 2 |
#define | FSL_TYPE_MINC 4 |
#define | FSL_TYPE_ANALYZE_GZ 100 |
#define | FSL_TYPE_NIFTI_GZ 101 |
#define | FSL_TYPE_NIFTI_PAIR_GZ 102 |
#define | FSL_TYPE_MINC_GZ 104 |
#define | FSL_RADIOLOGICAL -1 |
#define | FSL_NEUROLOGICAL 1 |
Typedefs | |
typedef unsigned char | THIS_UINT8 |
typedef char | THIS_INT8 |
typedef unsigned short | THIS_UINT16 |
typedef short | THIS_INT16 |
typedef unsigned int | THIS_UINT32 |
typedef int | THIS_INT32 |
typedef unsigned long | THIS_UINT64 |
typedef long | THIS_INT64 |
typedef float | THIS_FLOAT32 |
typedef double | THIS_FLOAT64 |
Functions | |
FSLIO * | FslOpen (const char *filename, const char *opts) |
Opens a file for either reading or writing. | |
FSLIO * | FslXOpen (const char *filename, const char *opts, int filetype) |
Opens a file for either reading or writing. | |
int | FslSeekVolume (FSLIO *fslio, size_t vols) |
int | FslClose (FSLIO *fslio) |
Write header and image data if this dataset was open for writing. Close the dataset header and data files. | |
void * | FslReadAllVolumes (FSLIO *fslio, char *filename) |
Read the header and all data into the FSLIO structure. | |
void | FslWriteAllVolumes (FSLIO *fslio, const void *buffer) |
Writes all data from buffer (using size info from fslio) to file. | |
size_t | FslReadVolumes (FSLIO *fslio, void *buffer, size_t nvols) |
Read the first nvols Volumes from a 4D dataset. | |
size_t | FslWriteVolumes (FSLIO *fslio, const void *buffer, size_t nvols) |
Write the first nvols volumes in buffer to disk. | |
void | FslWriteHeader (FSLIO *fslio) |
Writes nifti/anz header and opens img file ready for writing. | |
int | FslFileExists (const char *filename) |
char * | FslMakeBaseName (const char *fname) |
int | FslCheckForMultipleFileNames (const char *filename) |
int | FslGetEnvOutputType (void) |
void | FslSetIgnoreMFQ (int flag) |
int | FslGetIgnoreMFQ (void) |
void | FslSetOverrideOutputType (int type) |
int | FslGetOverrideOutputType (void) |
int | FslGetFileType (const FSLIO *fslio) |
void | FslSetFileType (FSLIO *fslio, int filetype) |
int | FslIsSingleFileType (int filetype) |
int | FslIsCompressedFileType (int filetype) |
int | FslBaseFileType (int filetype) |
char * | FslFileTypeString (int filetype) |
Return a string describing the format of the dataset. | |
int | FslGetWriteMode (const FSLIO *fslio) |
void | FslSetWriteMode (FSLIO *fslio, int mode) |
void | AvwSwapHeader (struct dsr *avw) |
int | FslReadRawHeader (void *buffer, const char *filename) |
FSLIO * | FslInit (void) |
allocate space for the FSLIO struct and set some sensible defaults | |
void | FslInitHeader (FSLIO *fslio, short t, size_t x, size_t y, size_t z, size_t v, float vx, float vy, float vz, float tr, size_t dim, const char *units) |
void | FslSetInit (FSLIO *fslio) |
void | FslCloneHeader (FSLIO *dest, const FSLIO *src) |
size_t | FslGetVolSize (FSLIO *fslio) |
void | FslSetDim (FSLIO *fslio, short x, short y, short z, short v) |
void | FslGetDim (FSLIO *fslio, short *x, short *y, short *z, short *v) |
void | FslSetDimensionality (FSLIO *fslio, size_t dim) |
void | FslGetDimensionality (FSLIO *fslio, size_t *dim) |
void | FslSetVoxDim (FSLIO *fslio, float x, float y, float z, float tr) |
void | FslGetVoxDim (FSLIO *fslio, float *x, float *y, float *z, float *tr) |
void | FslGetCalMinMax (FSLIO *fslio, float *min, float *max) |
void | FslSetCalMinMax (FSLIO *fslio, float min, float max) |
void | FslGetAuxFile (FSLIO *fslio, char *aux_file) |
void | FslSetAuxFile (FSLIO *fslio, const char *aux_file) |
void | FslSetTimeUnits (FSLIO *fslio, const char *units) |
void | FslGetTimeUnits (FSLIO *fslio, char *units) |
void | FslSetDataType (FSLIO *fslio, short t) |
size_t | FslGetDataType (FSLIO *fslio, short *t) |
int | FslGetIntensityScaling (FSLIO *fslio, float *slope, float *intercept) |
void | FslSetIntent (FSLIO *fslio, short intent_code, float p1, float p2, float p3) |
short | FslGetIntent (FSLIO *fslio, short *intent_code, float *p1, float *p2, float *p3) |
short | FslGetStdXform (FSLIO *fslio, mat44 *stdmat) |
void | FslSetStdXform (FSLIO *fslio, short sform_code, mat44 stdmat) |
void | FslGetMMCoord (mat44 stdmat, float voxx, float voxy, float voxz, float *mmx, float *mmy, float *mmz) |
void | FslGetVoxCoord (mat44 stdmat, float mmx, float mmy, float mmz, float *voxx, float *voxy, float *voxz) |
short | FslGetRigidXform (FSLIO *fslio, mat44 *rigidmat) |
void | FslSetRigidXform (FSLIO *fslio, short qform_code, mat44 rigidmat) |
int | FslGetLeftRightOrder (FSLIO *fslio) |
void | FslSetAnalyzeSform (FSLIO *fslio, const short *orig, float dx, float dy, float dz) |
void | FslGetAnalyzeOrigin (FSLIO *fslio, short orig[5]) |
size_t | FslReadSliceSeries (FSLIO *fslio, void *buffer, short slice, size_t nvols) |
Read one slice from each of the first nvols volumes in the dataset, ie get an xyt buffer. | |
size_t | FslReadRowSeries (FSLIO *fslio, void *buffer, short row, short slice, size_t nvols) |
Read one row from one slice for first nvols volumes in dataset; ie get an xt buffer. | |
size_t | FslReadTimeSeries (FSLIO *fslio, void *buffer, short xVox, short yVox, short zVox, size_t nvols) |
Read one voxel (xyz location) from first nvols volumes in dataset; ie get a t dim buffer. | |
mat33 | mat44_to_mat33 (mat44 x) |
FSLIO * | FslReadHeader (char *fname) |
Reads nifti/anz header, no data is read. | |
double **** | FslGetBufferAsScaledDouble (FSLIO *fslio) |
Return the fslio data buffer of a 1-4D dataset as a 4D array of scaled doubles. | |
double *** | FslGetVolumeAsScaledDouble (FSLIO *fslio, int vol) |
Return volume #vol (0-based) as a 3D array of scaled doubles. | |
int | convertBufferToScaledDouble (double *outbuf, void *inbuf, long len, float slope, float inter, int nifti_datatype) |
allocate a 4D buffer, use 1 contiguous buffer for the data | |
double **** | d4matrix (int th, int zh, int yh, int xh) |
allocate a 4D buffer, use 1 contiguous buffer for the data | |
double *** | d3matrix (int zh, int yh, int xh) |
allocate a 3D buffer, use 1 contiguous buffer for the data |
Data structures for using the fslio API. Written by Mark Jenkinson, FMRIB.
int convertBufferToScaledDouble | ( | double * | outbuf, |
void * | inbuf, | ||
long | len, | ||
float | slope, | ||
float | inter, | ||
int | nifti_datatype | ||
) |
allocate a 4D buffer, use 1 contiguous buffer for the data
Array is indexed as buf[0..th-1][0..zh-1][0..yh-1][0..xh-1].
To access all elements as a vector, use buf[0][0][0][i] where i can range from 0 to th*zh*yh*xh - 1.
outbuf | pointer to array of doubles of size len |
inbuf | void pointer to an array of len items of datatype nifti_datatype |
len | number of elements in outbuf and inbuf |
slope | slope term of scaling to be applied |
inter | intercept term of scaling to be applied: out = (in*slope)+inter |
nifti_datatype | NIFTI datatype code for the datatype of the elements in inbuf |
fill the buffer
double*** d3matrix | ( | int | zh, |
int | yh, | ||
int | xh | ||
) |
allocate a 3D buffer, use 1 contiguous buffer for the data
Array is indexed as buf[0..zh][0..yh][0..xh].
To access all elements as a vector, use buf[0][0][i] where i can range from 0 to zh*yh*xh - 1. Adaptation of Numerical Recipes in C nrutil.c allocation routines.
zh | slowest changing dimension |
yh | 2nd fastest changing dimension |
xh | fastest changing dimension |
allocate pointers to slices
allocate pointers for ydim
allocate the data blob
point everything to the data blob
double**** d4matrix | ( | int | th, |
int | zh, | ||
int | yh, | ||
int | xh | ||
) |
allocate a 4D buffer, use 1 contiguous buffer for the data
Array is indexed as buf[0..th][0..zh][0..yh][0..xh].
To access all elements as a vector, use buf[0][0][0][i] where i can range from 0 to th*zh*yh*xh - 1. Adaptation of Numerical Recipes in C nrutil.c allocation routines.
th | slowest changing dimension |
zh | 2nd slowest changing dimension |
yh | 2nd fastest changing dimension |
xh | fastest changing dimension |
allocate pointers to vols
allocate pointers to slices
allocate pointers for ydim
allocate the data blob
point everything to the data blob
Write header and image data if this dataset was open for writing. Close the dataset header and data files.
fslio | pointer to FSLIO data structure |
----- if writing the image, need to worry about the header bit -----
char* FslFileTypeString | ( | int | filetype | ) |
Return a string describing the format of the dataset.
filetype | FSL data format code. Legal values are as defined by FSL_TYPE. |
double**** FslGetBufferAsScaledDouble | ( | FSLIO * | fslio | ) |
Return the fslio data buffer of a 1-4D dataset as a 4D array of scaled doubles.
Array is indexed as buf[0..tdim-1][0..zdim-1][0..ydim-1][0..xdim-1].
The array will be byteswapped to native-endian.
Array values are scaled as per fslio header slope and intercept fields.
fslio | pointer to open dataset |
allocate new 4D buffer
cvt it
double*** FslGetVolumeAsScaledDouble | ( | FSLIO * | fslio, |
int | vol | ||
) |
Return volume #vol (0-based) as a 3D array of scaled doubles.
Volume Array is indexed as [0..zdim-1][0..ydim-1][0..xdim-1].
The array will be byteswapped to native-endian.
Array values are scaled as per fslio header slope and intercept fields.
fslio | pointer to open dataset |
vol | volume number to read (legal range [0..tdim-1]) |
allocate new 3D buffer
read in the data in disk format
cvt disk buffer to scaled double buffer
Opens a file for either reading or writing.
The format of the output dataset is determined automatically by passing filetype -1 to FslXOpen.
void* FslReadAllVolumes | ( | FSLIO * | fslio, |
char * | filename | ||
) |
Read the header and all data into the FSLIO structure.
There is no need for FslOpen or FslClose calls when FslReadAllVolumes() is called.
This routine allocates the buffer to hold the entire dataset.
The data block returned will contain the data in whatever datatype it is stored as on disk (therefore it is a void *).
The data buffer will be byteswapped to native-endian.
The data buffer will not be scaled.
The best call to make before this is FslInit() or a calloc() for fslio. (??? why calloc if this allocates the buffer ???)
fslio | pointer to an open dataset |
filename | Name of the dataset to read. |
otherwise it is a nifti file - so read it!
FSLIO* FslReadHeader | ( | char * | fname | ) |
Reads nifti/anz header, no data is read.
fname | filename specification (could be .img,.hdr,.nii, or no ext |
get header file name
read header information
size_t FslReadRowSeries | ( | FSLIO * | fslio, |
void * | buffer, | ||
short | row, | ||
short | slice, | ||
size_t | nvols | ||
) |
Read one row from one slice for first nvols volumes in dataset; ie get an xt buffer.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: filepointer in file data array is restored to its initial position.
fslio | pointer to open dataset |
buffer | buffer to hold one row from each volume. |
row | row number (0 based) to read [0 y-1] |
slice | slice number (0 based) to read |
nvols | number of volumes to read a row from |
size_t FslReadSliceSeries | ( | FSLIO * | fslio, |
void * | buffer, | ||
short | slice, | ||
size_t | nvols | ||
) |
Read one slice from each of the first nvols volumes in the dataset, ie get an xyt buffer.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: filepointer in file data array is restored to its initial position.
fslio | pointer to open dataset |
buffer | buffer large enough to hold 1 slice from each volume |
slice | slice number (0 based) to read [0 z-1] |
nvols | number of volumes to read a slice from |
size_t FslReadTimeSeries | ( | FSLIO * | fslio, |
void * | buffer, | ||
short | xVox, | ||
short | yVox, | ||
short | zVox, | ||
size_t | nvols | ||
) |
Read one voxel (xyz location) from first nvols volumes in dataset; ie get a t dim buffer.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: filepointer in file data array is restored to its initial position.
fslio | pointer to open dataset |
buffer | buffer to hold one timeseries vector |
xVox | x voxel [0 x-1] |
yVox | y voxel [0 y-1] |
zVox | z voxel [0 z-1] |
nvols | number of volumes to read a voxel from |
size_t FslReadVolumes | ( | FSLIO * | fslio, |
void * | buffer, | ||
size_t | nvols | ||
) |
Read the first nvols Volumes from a 4D dataset.
fslio | pointer to open dataset |
buffer | buffer to read data into, allocated by ??? |
nvols | number of volumes to read |
void FslWriteAllVolumes | ( | FSLIO * | fslio, |
const void * | buffer | ||
) |
Writes all data from buffer (using size info from fslio) to file.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: If file format is Analyze (not nifti) and in Neurological order then SWAP DATA into Radiological order.
fslio | pointer to open dataset |
buffer | pointer to data array. Size and datatype of this buffer |
void FslWriteHeader | ( | FSLIO * | fslio | ) |
Writes nifti/anz header and opens img file ready for writing.
fslio | pointer to open dataset |
size_t FslWriteVolumes | ( | FSLIO * | fslio, |
const void * | buffer, | ||
size_t | nvols | ||
) |
Write the first nvols volumes in buffer to disk.
Dimension and datatype of buffer are as is specified in nifti_image structure fslio->niftiptr. Note: If file format is Analyze (not nifti) and in Neurological order then SWAP DATA into Radiological order.
fslio | pointer to open dataset |
buffer | pointer to data array. Size and datatype of this buffer |
nvols | number of volumes to write |
Opens a file for either reading or writing.
Files to be read are automatically read whether compressed or not. Also, reading uses the file extension and will fail if that file does not exist. For a more robust read, pass the basename in as then all types will be tried.
filename | Name (or basename) of the file to open |
opts | Flags for fopen() of dataset, eg "r", "wb", etc. |
filetype | specifies the type of file to be written. Legal values are as defined by FSL_TYPE. If filetype is less than zero, then it is ignored and the type is determined by the filename extension or, failing that, the environment default. |
====================== Open file for writing ======================
======================== Open file for reading ======================