Cfitsio Toolkit - Manual


Introduction

The GNU Octave CFITSIO toolkit is a set of functions for manipulating Flexible Image Transport System (FITS) files for GNU Octave.

Table of Contents


1 Installing and loading

The GNU Octave CFITSIO toolkit must be installed and then loaded to be used.

It can be installed in GNU Octave directly from octave-cfitsio, or can be installed in an off-line mode via a downloaded tarball.

The toolkit has a dependency on the cfitsio library (https://heasarc.gsfc.nasa.gov/fitsio/), so it must be installed in order to successfully install the GNU Octave toolkit.

For Fedora: yum install cfitsio-devel

The toolkit must be then be loaded once per each GNU Octave session in order to use its functionality.

1.1 Windows install

If running in Windows, the package may already be installed, to check run:

pkg list cfitsio

Otherwise it can be installed by installing the requirements and then using the online or offline install method.

1.2 Online Direct install

With an internet connection available, the package can be installed from octave-cfitsio using the following command within GNU Octave:

pkg install "https://github.com/gnu-octave/octave-/cfitsioreleases/download/v0.0.7/octave-cfitsio-0.0.7.tar.gz"

On GNU Octave 7 and higher, the package can be installed in the simpler form of:

pkg install -forge cfitsio

The latest released version of the toolkit will be downloaded and installed.

1.3 Off-line install

With the toolkit package already downloaded, and in the current directory when running GNU Octave, the package can be installed using the following command within GNU Octave:

pkg install octave-cfitsio-0.0.7.tar.gz

1.4 Loading

Regardless of the method of installing the toolkit, in order to use its functions the toolkit must be loaded using the pkg load command:

pkg load cfitsio

The toolkit must be loaded on each GNU Octave session.


2 Basic Usage Overview

2.1 Overview

The octave-cfitsio toolkit provides high and low level functionality for reading and writing FITS format files.

The high level functions provide base read and write of data to octave using the functions fitsdisp, fitsinfo, fitsread and fitswrite. The low level functions provide direct access to the cfitsio API and are provided under the matlab.io.fits namespace. The low level functions provide access to the low level API of the CFITSIO C library (https://heasarc.gsfc.nasa.gov/fitsio/).

Since GNU Octave does not support the matlab import command, an import_fits function is provided.

Running the statement:

import_fits

Is the equivalent of running in matlab:

import matlab.io.fits;

2.2 Using the toolkit

The package must be loaded each time a GNU Octave session is started:

pkg load cfitsio

After loading the toolkit, the toolkit functions are available.

2.2.1 Reading Data

To read the primary image data of a fits file, use the fitsread function:

  imagedata = fitsread("thefitsfile.fits");

2.2.2 Reading Information

To read information about the content in a fits file, use the fitsinfo functions.

  info = fitsinfo("thefitsfile.fits");

2.2.3 Low level functionality

Where functionality is required that is not met by the high level functions, most of the cfitsio functions are available in the matlab.io.fits namespace.

Knowledge of the CFITSIO c library is beneficial in using the low level functions.

  # import the fits functions so don't have to use the full namespace each time
  import_fits;
  # open the file
  fd = fits.openFile('tst0012.fits');
  # get number of hdus in the file
  n = fits.getNumHDUs (fd);
  # for each hdu, go to it, print out the type
  for j = 1:n
    hdutype = fits.movAbsHDU (fd, j);
    printf ('HDU %d:  "%s"\n', j, hdutype);
  endfor
  # close the file
  fits.closeFile (fd);

3 Function Reference

The functions currently available in the toolkit are described below:


3.1 High Level File Functions

3.1.1 fitsdisp

: info = fitsdisp(filename)
: info = fitsdisp(filename, propertyname, propertyvalue)

Display metadata about fits format file

Inputs

filename - filename to open.

propertyname, propertyvalue - property name/value pairs

Known property names are:

’Index’

Value is a scalar or vector of hdu numbers to display

’Mode’

display mode of ’standard’ (default), ’min’ or ’full’

’standard’ display mode shows the standard keywords for the selected HDUs.
’min’ display mode shows only the type and size of the selected HDUs.
’full’ display shows all keywords for the selected HDU.

Outputs

info - the metadata of the file. If no output variable is provided, it displays to the screen.

Examples

 filename = file_in_loadpath("demos/tst0012.fits");
 fitsdisp(filename);

3.1.2 fitsinfo

: info = fitsinfo(filename)

Read information about fits format file

Inputs

filename - filename to open.

Outputs

info - a struct containing the structure and information about the fits file.

Examples

 filename = file_in_loadpath("demos/tst0012.fits");
 info = fitsinfo(filename);

3.1.3 fitsread

: data = fitsread(filename)
: data = fitsread(filename, 'raw')
: data = fitsread(filename, extname)
: data = fitsread(filename, extname, index)
: data = fitsread(filename, ____, propertyname, propertyvalue)

Read the primary data, or specified extension data. It scales the data and applied Nan to any undefined values.

Inputs

filename - filename to open.

exttype - can be ’primary’, ’asciitable’, ’binarytable’, ’image’, ’unknown’.

index - can be used to specify which table when more than one of a given type exists.

’raw’- If the ’raw’ keyword is used, the raw data from the file will be used without replacing undefined values with Nan

Known property names are:

Info

input info from fitsinfo call.

PixelRegion

pixel region to extract data for in an image. It expects a cell array of same size as the number of axis in the image. Each cell should be in vector format of: start, [start stop] or [start, increment, stop].

TableColumns

A list of columns to extract from a ascii or binary table.

TableRows

A list of rows to extract from an ascii or binary table.

Outputs

data - The read data from the table or image.

Examples

 filename = file_in_loadpath("demos/tst0012.fits");
 # read the primary image data
 imagedata = fitsread(filename);
 # read the 1st non primary image
 imagedata = fitsread(filename, "image");
 # read the first binary table, selected columns
 tbldata = fitsread(filename, "binarytable", "TableColumns", [1 2 11]);
 # read the first ascii table
 atbldata = fitsread(filename, "asciitable");

3.1.4 fitswrite

: fitswrite(data, filename)
: fitswrite(data, filename, propertyname, propertyvalue)

Write image data data to FITS file filename. If the fie already exists, overwrite it.

Inputs

data - imagedata to write to a file.

filename - filename to write to.

propertyname, propertyvalue - property name/value pairs

Additional properties can be set as propertyname, propertyvalue pairs. Known property names are:

WriteMode

Set mode for writing to image as ’overwrite’ (default) or ’append’ to append images.

Compression

Set compression type to use for image as ’none’ (default), ’gzip’, ’rice’, ’hcompress’ or ’plio’.

Outputs

None

Examples

 filename = tempname();
 X =  double([1:3;4:6]);
 fitswrite(X, filename);

3.2 Low Level File Functions

3.2.1 matlab.io.fits.closeFile

: closeFile(file)

Close the opened fits file

This is the equivalent of the fits_close_file function.

Inputs

file - opened file returned from openFile or createFile.

Outputs

None

Examples

 import_fits;
 filename = file_in_loadpath("demos/tst0012.fits")
 fd = fits.openFile(filename);
 fits.closeFile(fd);

See also: matlab.io.fits.createFile, matlab.io.fits.openFile.

3.2.2 matlab.io.fits.createFile

: file = createFile(filename)

Attempt to create a file of the given input name.

If the filename starts with ! and the file exists, it will create a new file, otherwise, if the file exists, the create will fail.

This is the equivalent of the cfitsio fits_create_file function.

Inputs

filename - filename to open.

Outputs

file - opened file identifier.

Examples

 import_fits;
 fd = fits.createFile("myfitsfile.fits");
 fits.createImg(fd, 'uint16', [100 100]);
 fits.closeFile(fd);

See also: matlab.io.fits.openFile.

3.2.3 matlab.io.fits.deleteFile

: deleteFile(file)

Force a close and delete of a fits file.

This is the equivalent of the fits_delete_file function.

Inputs

file - opened fits file.

Outputs

None

3.2.4 matlab.io.fits.fileMode

: mode = fileMode(file)

Return the file mode of the opened fits file.

This is the equivalent of the fits_file_mode function.

Inputs

file - opened fits file.

Outputs

mode - The mode will return as a string ’READWRITE’ or ’READONLY’

3.2.5 matlab.io.fits.fileName

: filename = fileName(file)

Return the file name of the opened fits file.

This is the equivalent of the fits_file_name function.

Inputs

file - opened fits file.

Outputs

filename - name of the fits file.

3.2.6 matlab.io.fits.openDiskFile

: file = openDiskFile(filename)
: file = openDiskFile(filename, mode)

Attempt to open a file of the given input name, ignoring any special processing of the filename.

This is the equivalent of the cfitsio fits_open_diskfile function.

Inputs

filename - filename to open.

mode - If the option mode string ’READONLY’ (default) or ’READWRITE’ is provided, open the file using that mode.

Outputs

file - opened file identifier.

Examples

 import_fits;
 filename = file_in_loadpath("demos/tst0012.fits")
 fd = fits.openDiskFile(filename, 'READONLY');
 fits.closeFile(fd);

See also: openFile, createFile.

3.2.7 matlab.io.fits.openFile

: file = openFile(filename)
: file = openFile(filename, mode)

Attempt to open a file of the given input name.

This is the equivalent of the cfitsio fits_open_file function.

Inputs

filename - filename to open.

mode - If the option mode string ’READONLY’ (default) or ’READWRITE’ is provided, open the file using that mode.

Outputs

file - opened file identifier.

Examples

 import_fits;
 filename = file_in_loadpath("demos/tst0012.fits")
 fd = fits.openFile(filename, 'READONLY');
 fits.closeFile(fd);

See also: matlab.io.fits.openDiskFile, matlab.io.fits.createFile.


3.3 Low Level HDU Functions

3.3.1 matlab.io.fits.copyHDU

: copyHDU(infile, outfile)

Copy current HDU from one infile to another.

This is the equivalent of the cfitsio fits_copy_hdu function.

Inputs

filename - filename to open.

Outputs

infile - opened input file identifier.

outfile - opened output file identifier.

Examples

 import_fits;
 # open input and output files
 infilename = file_in_loadpath("demos/tst0012.fits");
 infile = fits.openFile(infilename);
 outfile = fits.createFile("myfitsfile.fits");
 # copy first hdu
 fits.copyHDU(infile, outfile);
 # move to and then copy 2nd hdu
 fits.movAbsHDU(infile,2);
 fits.copyHDU(infile, outfile);
 # close files
 fits.closeFile(infile);
 fits.closeFile(outfile);

3.3.2 matlab.io.fits.deleteHDU

: type = deleteHDU(file)

Delete the current HDU and go to next HDU.

Returns the newly current HDU type as a string.

This is the equivalent of the cfitsio fits_delete_hdu function.

Inputs

file - opened fits file.

Outputs

type - string value for type of the next HDU.

3.3.3 matlab.io.fits.getHDUnum

: num = getHDUnum(file)

Return the index of the current HDU.

This is the equivalent of the cfitsio fits_get_hdu_num function.

Inputs

file - opened fits file.

Outputs

num - current hdu number.

3.3.4 matlab.io.fits.getHDUoff

: [headtstart, datastart, dataend] = getHDUoff(file)

Return offsets of the current HDU.

This is the equivalent of the cfitsio fits_get_hduoff function.

Inputs

file - opened fits file.

Outputs

headtstart, datastart, dataend - offset information for the current HDU.

3.3.5 matlab.io.fits.getHDUtype

: type = getHDUtype(file)

Return the current HDUs type as a string.

This is the equivalent of the cfitsio fits_get_hdu_type function.

Inputs

file - opened fits file.

Outputs

type - current hdu type

3.3.6 matlab.io.fits.getNumHDUs

: num = getNumHDUs(file)

Return the count of HDUs in the file.

This is the equivalent of the cfitsio fits_get_num_hdus function.

Inputs

file - opened fits file.

Outputs

num - return the number of HDUs in the file.

Examples

 import_fits;
 testname = file_in_loadpath("demos/tst0012.fits");
 fd = fits.openFile(testname);
 hducount = getNumHDUs(fd), 5);
 fits.closeFile(fd);

3.3.7 matlab.io.fits.movAbsHDU

: type = movAbsHDU(file, hdunum)

Go to absolute HDU index hdunum

Returns the newly current HDU type as a string.

This is the equivalent of the cfitsio fits_movabs_hdu function.

Inputs

file - opened fits file.

hdunum - HDU number to move to.

Outputs

type - hdu type of the now current HDU.

3.3.8 matlab.io.fits.movNamHDU

: hdutype = movNamHDU(file, hdutype, extname, extver)

Go to HDU matching hdutype, extname, extver.

This is the equivalent of the cfitsio fits_movnam_hdu function.

Inputs

file - opened fits file.

hdutype - HDU number to move to. Valid hdutype values are ’IMAGE_HDU’, ’ASCII_TBL’, ’BINARY_TBL’, ’ANY_HDU’.

extname, extver - EXTNAME and EXTVER keywords to match.

Outputs

hdutype - hdu type of the now current HDU.

3.3.9 matlab.io.fits.movRelHDU

: type = movRelHDU(file, hdunum)

Go to relative HDU index hdunum.

Returns the newly current HDU type as a string.

This is the equivalent of the cfitsio fits_movrel_hdu function.

Inputs

file - opened fits file.

hdunum - relative HDU number to move to.

Outputs

type - hdu type of the now current HDU.

3.3.10 matlab.io.fits.writeChecksum

: writeChecksum(file)

Recalculate the HDU checksum and if required, write the new value.

This is the equivalent of the cfitsio fits_write_chksum function.

Inputs

file - opened fits file.

Outputs

None


3.4 Low Level Keyword Functions

3.4.1 matlab.io.fits.deleteKey

: deleteKey(file, key)

Delete a key in the fits file.

This is the equivalent of the cfitsio fits_delete_key function.

Inputs

file - opened fits file.

key - Key name to remove.

Outputs

None

3.4.2 matlab.io.fits.deleteRecord

: deleteRecord(file, keynum)

Delete a key in the fits file.

This is the equivalent of the cfitsio fits_delete_record function.

Inputs

file - opened fits file.

keynum - Record number to remove.

Outputs

None

3.4.3 matlab.io.fits.getHdrSpace

: [numkeys, freekeys] = getHdrSpace(file)

Get the number of keyword records used and available.

This is the equivalent of the cfitsio fits_get_hdrspace function.

Inputs

file - opened fits file.

Outputs

numkeys - number of existing keys.

freekeys - number of free key space.

3.4.4 matlab.io.fits.readCard

: card = readCard(file, recname)

Read the keyword card for name recname

This is the equivalent of the cfitsio fits_read_card function.

Inputs

file - opened fits file.

recname - record name to read

Outputs

card - unparsed record value string

3.4.5 matlab.io.fits.readKey

: [keyvalue, keycomment] = readKey(file, recname)

Read the keyword value and comment for name recname.

This is the equivalent of the cfitsio fits_read_key_str function.

Inputs

file - opened fits file.

recname - keyword name.

Outputs

keyvalue - string value of record.

keycomment - comment string

3.4.6 matlab.io.fits.readKeyCmplx

: [value, comment] = readKeyCmplx(file, recname)

Read the key value recname as a complex double.

This is the equivalent of the cfitsio fits_read_key_dblcmp function.

Inputs

file - opened fits file.

recname - keyword name.

Outputs

value - complex value of record.

comment - comment string

3.4.7 matlab.io.fits.readKeyDbl

Function File: [value, comment] = readKeyDbl(file, recname)

Read the key value recname as a double.

This is the equivalent of the cfitsio fits_read_key_dbl function.\n \

Inputs

file - opened fits file.

recname - keyword name.

Outputs

value - double value of record.

comment - comment string

3.4.8 matlab.io.fits.readKeyLongLong

: [value, comment] = readKeyLongLong(file, recname)

Read the key value recname as a long long.

This is the equivalent of the cfitsio fits_read_key_lnglng function.

Inputs

file - opened fits file.

recname - keyword name.

Outputs

value - int64 value of record.

comment - comment string

3.4.9 matlab.io.fits.readKeyLongStr

: [value, comment] = readKeyLongStr(file, recname)

Read the key value recname as a string.

This is the equivalent of the cfitsio fits_read_key_longstr function.

Inputs

file - opened fits file.

recname - keyword name.

Outputs

value - string value of record.

comment - comment string

3.4.10 matlab.io.fits.readKeyUnit

: keyunit = readKeyUnit(file, recname)

Read the physical key units value recname.

This is the equivalent of the cfitsio fits_read_key_unit function.

Inputs

file - opened fits file.

recname - keyword name.

Outputs

keyunit - units value of record.

3.4.11 matlab.io.fits.readRecord

: rec = readRecord(file, recidx)

Read the keyword record at recidx.

This is the equivalent of the cfitsio fits_read_record function.

Inputs

file - opened fits file.

recidx - record number.

Outputs

rec - full keyword record

3.4.12 matlab.io.fits.writeComment

: writeComment(file, comment)

Append a comment to to the fits file.

This is the equivalent of the cfitsio fits_write_comment function.

Inputs

file - opened fits file.

comment - comment to append

Outputs

None

3.4.13 matlab.io.fits.writeDate

: writeDate(file)

Write the date keyword.

This is the equivalent of the cfitsio fits_write_date function.

Inputs

file - opened fits file.

Outputs

None

3.4.14 matlab.io.fits.writeHistory

: writeHistory(file, history)

Append a history to to the fits file.

This is the equivalent of the cfitsio fits_write_history function.

Inputs

file - opened fits file.

history - history string.

Outputs

None

3.4.15 matlab.io.fits.writeKey

: writeKey(file, key, value)
: writeKey(file, key, value, comment)
: writeKey(file, key, value, comment, decimals)

Append or replace a key in the fits file.

This is the equivalent of the cfitsio fits_write_key and fits_update_key function.

Inputs

file - opened fits file.

key - keyword name.

value - keyword value.

comment - keyword comment.

decimals - number of decimals.

Outputs

None

3.4.16 matlab.io.fits.writeKeyUnit

: writeKeyUnit(file, key, unit)

Write a key unit to the fits file.

This is the equivalent of the cfitsio fits_write_key_unit function.

Inputs

file - opened fits file.

key - keyword name.

unit - keyword units as string.

Outputs

None


3.5 Low Level Image Manipulation

3.5.1 matlab.io.fits.createImg

: createImg(file, bitpix, naxis)

create a new primary image or image extension.

This is the equivalent of the cfitsio fits_create_imgll function.

Inputs

file - file previously opened with openFile, openDiskFile or createFile.

bitpix - type for the data as a string in either matlab or cfitsio naming.

naxis - axis values for the image.

Outputs

None

Examples

 import_fits;
 fd = fits.createFile("test.fits");
 fits.createImg(fd,'int16',[10 20]);
 fits.close(fd);

3.5.2 matlab.io.fits.getImgSize

: size = getImgSize(file)

Return size of a Image HDU.

This is the equivalent of the cfitsio fits_get_img_size function.

Inputs

file - opened fits file.

Outputs

size - vector containing the image dimensions.

3.5.3 matlab.io.fits.getImgType

: type = getImgType(file)

Return datatype of a Image HDU

This is the equivalent of the cfitsio fits_get_img_type function.

Inputs

file - opened fits file.

Outputs

type - datatype as a string for the image type.

3.5.4 matlab.io.fits.insertImg

: insertImg(file, bitpix, naxis)

Insert a new primary image or image extension at current HDU position.

This is the equivalent of the cfitsio fits_insert_imgll function.

Inputs

file - file previously opened with openFile, openDiskFile or createFile.

bitpix - type for the data as a string in either matlab or cfitsio naming.

naxis - axis values for the image.

Outputs

None

3.5.5 matlab.io.fits.readImg

: data = readImg(file)
: data = readImg(file, firstpix, lastpix)
: data = readImg(file, firstpix, lastpix, inc)

Read Image data.

This is the equivalent of the cfitsio fits_read_subset function.

Inputs

file - opened fits file.

firstpix - first pile coordinate

lastpix - last pixel coordinate

inc - pixel increment

Outputs

data - image data read

Examples

 import_fits;
 filename = file_in_loadpath("demos/tst0012.fits");
 fd = fits.openFile(filename);
 # read the image
 imagedata = fits.readImg(fd);
 # read a 70x80 part of the image
 imagedata = fits.readImg(fd, [11 11],[80 90]);
 fits.closeFile(fd);

3.5.6 matlab.io.fits.setBscale

: setBscale(file, bscale, bzero)

Reset bscale and bzero to be used with reading and writing Images.

This is the equivalent of the cfitsio fits_set_bscale function.

Inputs

file - opened fits file.

bscale - bscale value

bzero - bzero value

Outputs

None

3.5.7 matlab.io.fits.setTscale

: setTscale(file, col, scale, zero)

Reset scale and zero to be used with reading and writing table data.

This is the equivalent of the cfitsio fits_set_tscale function.

Inputs

file - opened fits file.

col - column number

scale - scale value

zero - zero value

Outputs

None

3.5.8 matlab.io.fits.writeImg

: writeImg(file, imagedata)
: writeImg(file, imagedata, fpixel)

write imagedata to a FITS file. The rows and column size must match the size of NAXIS, NAXIS etc

This is the equivalent of the cfitsio fits_write_subset function.

Inputs

file - opened fits file.

imagedata - Image data.

fpixel - start pixel to write from.

Outputs

None

Examples

Create a fits file and write a 10x10 image in the primary and image ext:

 import_fits;
 fd = fits.createFile("myfitsfile.fits");
 data = int16(zeros(10,10));
 # primary
 fits.createImg(fd,class(data), size(data));
 fits.writeImg(fd,data);
 # image ext
 fits.createImg(fd,class(data), size(data));
 fits.writeImg(fd,data);
 # close file
 fits.closeFile(fd);

3.6 Low Level Utility Functions

3.6.1 matlab.io.fits.getConstantNames

: namelist = getConstantNames()

Return the names of all known fits constants.

Inputs

None

Outputs

namelist - cell array of all known fits constant names

See also: getConstantValue.

3.6.2 matlab.io.fits.getConstantValue

: value = getConstantValue(name)

Return the value of a known fits constant.

Inputs

name - name of the constant to retrieve value of.

Outputs

value - value of the constant

See also: getConstantNames.

3.6.3 matlab.io.fits.getOpenFiles

: files = getOpenFiles()

Get the file handles of all open fits files.

Inputs

None

Outputs

files list of opened fits file handles.

See also: openFile.

3.6.4 matlab.io.fits.getVersion

: ver = getVersion()

Return the version number of the cfitsio library used.

This is the equivalent of the cfitsio fits_get_version function.

Inputs

file - opened fits file.

Outputs

ver - version


3.7 Low Level Compression Functions

3.7.1 matlab.io.fits.imgCompress

: imgCompress(infile, outfile)

Copy HDU and image data from one infile to another, using the outfiles compression type.

This is the equivalent of the cfitsio fits_img_compress function.

Inputs

infile - opened input fits file.

outfile - opened writable output fits file.

Outputs

None

3.7.2 matlab.io.fits.isCompressedImg

: comp = isCompressedImg(file)

Return true if image is compressed.

This is the equivalent of the cfitsio fits_is_compressed_image function.

Inputs

file - opened fits file.

Outputs

comp - boolean for whether image is compressed or not.

3.7.3 matlab.io.fits.setCompressionType

: setCompressionType(file, comptype)

Set compression type for writing FITS images.

This is the equivalent of the cfitsio fits_set_compression_type function.

Inputs

file - opened fits file.

comptype - compression type. Valid comptype values are: ’GZIP’, ’GZIP2’, ’RICE’, ’PLIO’, ’HCOMPRESS’ or ’NOCOMPRESS’.

Outputs

None

3.7.4 matlab.io.fits.setHCompScale

: setHCompScale(file, scale)

Set scale to be used with HCOMPRESS compression.

This is the equivalent of the cfitsio fits_set_hcomp_scale function.

Inputs

file - opened fits file.

scale - scale value

Outputs

None

3.7.5 matlab.io.fits.setHCompSmooth

: setHCompSmooth(file, smooth)

Set smooth value to be used with HCOMPRESS compression.

This is the equivalent of the cfitsio fits_set_hcomp_smooth function.

Inputs

file - opened fits file.

smooth - smooth value

Outputs

None

3.7.6 matlab.io.fits.setTileDim

: setTileDim(file, tiledims)

Set compression tile dims for writing FITS images.

This is the equivalent of the cfitsio fits_set_tile_dim function.

Inputs

file - opened fits file.

tiledims - tile dimensions

Outputs

None


3.8 Low Level Binary and ASCII Tables

3.8.1 matlab.io.fits.createTbl

: createTbl(file, tbltype, nrows, ttype, tform)
: createTbl(file, tbltype, nrows, ttype, tform, tunit)
: createTbl(file, tbltype, nrows, ttype, tform, tunit, extname)

Create a new ASCII or bintable extension.

This is the equivalent of the cfitsio fits_create_tbl function.

Inputs

file - opened fits file.

tbltype - table type ’binary’ or ’ascii’.

nrows - initial number of rows (normally 0)

ttype - cell array of column type

tform - cell array of column format

tunit - cell array of column units

extname - optional extension name

ttype, tform, tunit are expected to be the same size.

Outputs

None

Examples

 import_fits;
 fd = fits.createFile("test.fits");
 ttype = {'Col1','Col2','Col3','Col4'};
 tform = {'A9','A4','A3','A8'};
 tunit = {'m','s','kg','km'};
 fits.createTbl(fd,'binary',0,ttype,tform,tunit,'table-name');
 fits.closeFile(fd);

3.8.2 matlab.io.fits.deleteCol

: deleteCol(file, colnum)

Delete a column from a table.

This is the equivalent of the cfitsio fits_delete_col function.

Inputs

file - opened fits file.

colnum - Column to delete from current table.

Outputs

None

3.8.3 matlab.io.fits.deleteRows

: deleteRows(file, firstrow, numrows)

Insert a rows into a table.

This is the equivalent of the cfitsio fits_delete_rows function.

Inputs

file - opened fits file.

firstrow - Start row to delete.

numrows - Number of rows to delete.

Outputs

None

3.8.4 matlab.io.fits.getAColParms

: [ttype,tbcol,tunit,tform,scale,zero,nulstr,tdisp] = getAColParms(file, colnum)

Get ASCII table parameters.

This is the equivalent of the cfitsio fits_get_acolparms function.

Inputs

file - opened fits file.

colnum - Column to retrieve.

Outputs

ttype,tbcol,tunit,tform,scale,zero,nulstr,tdisp column information in same format as provided by fits_get_acolparms.

3.8.5 matlab.io.fits.getBColParms

: [ttype,tunit,typechar,repeat,scale,zero,nulval,tdisp] = getBColParms(file, colnum)

Get binary table parameters.

This is the equivalent of the cfitsio fits_get_bcolparms function.

Inputs

file - opened fits file.

colnum - Column to retrieve.

Outputs

ttype,tunit,typechar,repeat,scale,zero,nulval,tdisp column information in same format as provided by fits_get_bcolparms.

3.8.6 matlab.io.fits.getColName

: [colnum,colname] = getColName(file, template)
: [colnum,colname] = getColName(file, template, casesens)

Get column name.

This is the equivalent of the cfitsio fits_get_colname function.

Inputs

file - opened fits file.

template - template string for matching column name.

casesens - boolean whether to be case sensitive in match.

Outputs

colnum - column number of match.

colname - column name of match.

Examples

 import_fits;
 filename = file_in_loadpath("demos/tst0012.fits");
 fd = fits.openFile(filename);
 fits.movAbsHDU(fd,2);
 [colnum, colname] = fits.getColName(fd,"C*");
 # returned 3, "COUNTS"
 fits.closeFile(fd);

3.8.7 matlab.io.fits.getColType

: [dtype,repeat,width] = getColType(file, colnum)

Get column type.

This is the equivalent of the cfitsio fits_get_coltypell function.

Inputs

file - opened fits file.

colnum - Column to delete from current table.

Outputs

dtype,repeat,width - column information.

3.8.8 matlab.io.fits.getEqColType

: [dtype,repeat,width] = getEqColType(file, colnum)

Get column type.

This is the equivalent of the cfitsio fits_get_eqcoltypell function.

Inputs

file - opened fits file.

colnum - Column number.

Outputs

dtype,repeat,width - column type

3.8.9 matlab.io.fits.getNumCols

: ncols = getNumCols(file)

Get number of columns.

This is the equivalent of the cfitsio fits_get_num_cols function.

Inputs

file - opened fits file.

Outputs

ncols - the number of columns in the table.

3.8.10 matlab.io.fits.getNumRows

: nrows = getNumRows(file)

Get number of rows.

This is the equivalent of the cfitsio fits_get_numrowsll function.

Inputs

file - opened fits file.

Outputs

nrows - the number of rows in in the current table.

3.8.11 matlab.io.fits.getRowSize

: nrows = getRowSize(file)

Get optimum number of rows to read/write at one time.

This is the equivalent of the cfitsio fits_get_rowsize function.

Inputs

file - opened fits file.

Outputs

nrows - number of rows.

3.8.12 matlab.io.fits.insertATbl

: insertATbl(file, rowlen, nrows, ttype, tbcol, tform)
: insertATbl(file, rowlen, nrows, ttype, tbcol, tform, tunit)
: insertATbl(file, tbltype, nrows, ttype, tbcol, tform, tunit, extname)

Insert a new ASCII table after current HDU.

This is the equivalent of the cfitsio fits_insert_atbl function.

Inputs

file - opened fits file.

rowlen - row length. If set to 0, the function will calculate size based on tbcol and ttype.

nrows - initial number of rows (normally 0)

ttype - cell array of column type

tbcol - array containing the start indices for each column.

tform - cell array of column format

tunit - cell array of column units

extname - optional extension name

Outputs

None

3.8.13 matlab.io.fits.insertBTbl

: insertBTbl(file, nrows, ttype, tform, tunit, extname, pcount)

Insert a new bintable extension.

This is the equivalent of the cfitsio fits_insert_btbl function.

Inputs

file - opened fits file.

nrows - initial number of rows (normally 0)

ttype - cell array of column type

tform - cell array of column format

tunit - cell array of column units

extname - optional extension name

pcount - heap size.

ttype, tform, tunit are expected to be the same size.

Outputs

None

3.8.14 matlab.io.fits.insertCol

: insertCol(file, colnum, ttype, tform)

Insert a column into a table.

This is the equivalent of the cfitsio fits_insert_col function.

Inputs

file - opened fits file.

colnum - Column to delete from current table.

ttype, tform - column type to insert

Outputs

None

3.8.15 matlab.io.fits.insertRows

: insertRows(file, firstrow, numrows)

Insert rows into a table.

This is the equivalent of the cfitsio fits_insert_rows function.

Inputs

file - opened fits file.

firstrow - Start row to insert from.

numrows - Number of rows to add.

Outputs

None

3.8.16 matlab.io.fits.readATblHdr

: [rowlen,nrows,ttype,tbcol,tform,tunit,extname] = readATblHdr(file)

Get ASCII table parameters.

This is the equivalent of the cfitsio fits_read_atablhdrll function.

Inputs

file - opened fits file.

Outputs

rowlen,nrows,ttype,tbcol,tform,tunit,extname - table properties

3.8.17 matlab.io.fits.readBTblHdr

: [nrows,ttype,tform,tunit,extname,pcount] = readBTblHdr(file)

Get Binary table parameters.

This is the equivalent of the cfitsio fits_read_btablhdrll function.

Inputs

file - opened fits file.

Outputs

nrows,ttype,tform,tunit,extname,pcount] - table properties

3.8.18 matlab.io.fits.readCol

: [coldata, nullval] = readCol(file, colnum)
: [coldata, nullval] = readCol(file, colnum, firstrow, numrows)

Get table row data.

This is the equivalent of the cfitsio fits_read_col function.

Inputs

file - opened fits file.

firstrow - Start row

numrows - Number of rows to read

Outputs

coldata - the column data rows

nulldata - the null value flags

Examples

 import_fits;
 # open file
 filename = file_in_loadpath("demos/tst0012.fits");
 fd = fits.openFile(filename);
 # move to binary table and get column for flux
 fits.movAbsHDU(fd, 2);
 colnum = fits.getColName(fd, 'flux');
 # read all rows in column
 fluxdata = fits.readCol(fd, colnum);
 # read data starting at 2nd value
 fluxdata = fits.readCol(fd, colnum, 2);
 # read rows 3 rows starting at row 2
 fluxdata = fits.readCol(fd, colnum, 2, 3);
 fits.closeFile(fd);

3.8.19 matlab.io.fits.writeCol

: writeCol(file, colnum, firstrow, data)

Write elements to a table.

This is the equivalent of the cfitsio fits_write_col function.

Inputs

file - opened fits file.

colnum - column number.

firstrow - first row number.

data - data to write to column

Outputs

None


3.9 Import functions

3.9.1 import_fits

: import_fits

Import the fits functions into a fits.xxxxx variable, to emulate importing the fits namespace.


Appendix A GNU General Public License

Version 3, 29 June 2007
Copyright © 2007 Free Software Foundation, Inc. http://fsf.org/
Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.

Preamble

The GNU General Public License is a free, copyleft license for software and other kinds of works.

The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program—to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.

When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.

To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others.

For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.

Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it.

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Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users’ freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users.

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    A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.

    Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.

  13. No Surrender of Others’ Freedom.

    If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.

  14. Use with the GNU Affero General Public License.

    Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.

  15. Revised Versions of this License.

    The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.

    Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.

    If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy’s public statement of acceptance of a version permanently authorizes you to choose that version for the Program.

    Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.

  16. Disclaimer of Warranty.

    THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

  17. Limitation of Liability.

    IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

  18. Interpretation of Sections 15 and 16.

    If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.

END OF TERMS AND CONDITIONS

How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.

To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.

one line to give the program's name and a brief idea of what it does.  
Copyright (C) year name of author
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at
your option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program.  If not, see http://www.gnu.org/licenses/.

Also add information on how to contact you by electronic and paper mail.

If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:

program Copyright (C) year name of author 
This program comes with ABSOLUTELY NO WARRANTY; for details type ‘show w’.
This is free software, and you are welcome to redistribute it
under certain conditions; type ‘show c’ for details.

The hypothetical commands ‘show w’ and ‘show c’ should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.

You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see http://www.gnu.org/licenses/.

The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read http://www.gnu.org/philosophy/why-not-lgpl.html.


Index

Jump to:   B   C   D   F   G   H   I   L   M   O   R   S   U   W  
Index EntrySection

B
Basic Usage OverviewBasic Usage Overview

C
closeFileLow Level File Functions
copyHDULow Level HDU Functions
copyrightCopying
createFileLow Level File Functions
createImgLow Level Image Manipulation
createTblLow Level Binary and ASCII Tables

D
deleteColLow Level Binary and ASCII Tables
deleteFileLow Level File Functions
deleteHDULow Level HDU Functions
deleteKeyLow Level Keyword Functions
deleteRecordLow Level Keyword Functions
deleteRowsLow Level Binary and ASCII Tables

F
fileModeLow Level File Functions
fileNameLow Level File Functions
fitsdispHigh Level File Functions
fitsinfoHigh Level File Functions
fitsreadHigh Level File Functions
fitswriteHigh Level File Functions
Function ReferenceFunction Reference

G
getAColParmsLow Level Binary and ASCII Tables
getBColParmsLow Level Binary and ASCII Tables
getColNameLow Level Binary and ASCII Tables
getColTypeLow Level Binary and ASCII Tables
getConstantNamesLow Level Utility Functions
getConstantValueLow Level Utility Functions
getEqColTypeLow Level Binary and ASCII Tables
getHdrSpaceLow Level Keyword Functions
getHDUnumLow Level HDU Functions
getHDUoffLow Level HDU Functions
getHDUtypeLow Level HDU Functions
getImgSizeLow Level Image Manipulation
getImgTypeLow Level Image Manipulation
getNumColsLow Level Binary and ASCII Tables
getNumHDUsLow Level HDU Functions
getNumRowsLow Level Binary and ASCII Tables
getOpenFilesLow Level Utility Functions
getRowSizeLow Level Binary and ASCII Tables
getVersionLow Level Utility Functions

H
High Level File FunctionsHigh Level File Functions

I
imgCompressLow Level Compression Functions
Import functionsImport functions
import_fitsImport functions
insertATblLow Level Binary and ASCII Tables
insertBTblLow Level Binary and ASCII Tables
insertColLow Level Binary and ASCII Tables
insertImgLow Level Image Manipulation
insertRowsLow Level Binary and ASCII Tables
Installing and loadingInstalling and loading
isCompressedImgLow Level Compression Functions

L
LoadingInstalling and loading
Low Level Binary and ASCII TablesLow Level Binary and ASCII Tables
Low Level Compression FunctionsLow Level Compression Functions
Low Level File FunctionsLow Level File Functions
Low level functionalityBasic Usage Overview
Low Level HDU FunctionsLow Level HDU Functions
Low Level Image ManipulationLow Level Image Manipulation
Low Level Keyword FunctionsLow Level Keyword Functions
Low Level Utility FunctionsLow Level Utility Functions

M
movAbsHDULow Level HDU Functions
movNamHDULow Level HDU Functions
movRelHDULow Level HDU Functions

O
Off-line installInstalling and loading
Online installInstalling and loading
openDiskFileLow Level File Functions
openFileLow Level File Functions
OverviewBasic Usage Overview

R
readATblHdrLow Level Binary and ASCII Tables
readBTblHdrLow Level Binary and ASCII Tables
readCardLow Level Keyword Functions
readColLow Level Binary and ASCII Tables
readImgLow Level Image Manipulation
Reading DataBasic Usage Overview
Reading InformationBasic Usage Overview
readKeyLow Level Keyword Functions
readKeyCmplxLow Level Keyword Functions
readKeyDblLow Level Keyword Functions
readKeyLongLongLow Level Keyword Functions
readKeyLongStrLow Level Keyword Functions
readKeyUnitLow Level Keyword Functions
readRecordLow Level Keyword Functions

S
setBscaleLow Level Image Manipulation
setCompressionTypeLow Level Compression Functions
setHCompScaleLow Level Compression Functions
setHCompSmoothLow Level Compression Functions
setTileDimLow Level Compression Functions
setTscaleLow Level Image Manipulation

U
Using the toolkitBasic Usage Overview

W
warrantyCopying
Windows installInstalling and loading
writeChecksumLow Level HDU Functions
writeColLow Level Binary and ASCII Tables
writeCommentLow Level Keyword Functions
writeDateLow Level Keyword Functions
writeHistoryLow Level Keyword Functions
writeImgLow Level Image Manipulation
writeKeyLow Level Keyword Functions
writeKeyUnitLow Level Keyword Functions