PDL::IO::Nifti -- Module to access imaging data using Nifti-1 standard
use strict; use 5.10.0; use PDL; use PDL::IO::Nifti; use PDL::NiceSlice;
my $name=shift; my $file; say "testing write_nii()"; open $file,'>testnii.nii' or die "Cannot open file to write\n"; my $nii=PDL::IO::Nifti->new; # Creates the object $nii->img(rvals(64,32)); # Assigns data
# The following lines illustrate how to access PDLs $nii->img->()*=3000; $nii->img->(0,).=0; say avg $nii->img; say $nii->img->info;
# Now we write out the data $nii->write_nii($file); close $file;
#Now we read a file open my $file,$name or die "Failed to read $name\n"; my $ni2=$nii->new; $ni2->read_nii($file); say $ni2->img->info; $ni2->img->(,,0)->squeeze->wpic('nii.png');
Provides methods to read and write Nifti files, read, write and manipulate the header based on PDL.
my $nii=PDL::IO::Nifti->new($pdl); $nii->write_nii($file);
is all you need to do to save your data.
Initialize the object. Calls img if passed an argument.
This method should be called whenever you want to access your piddle. The first argument will replace your piddle with whatever it holds. It returns the piddle. This method should be used whenever you need to access your data.
$nii->read_nii($file); my $pdl=$nii->img;
can be used to load an image into $pdl.
Loads an existing .nii file. If you have an analyze image/hdr pair, please convert to nifti first. All elements are loaded and are accessible via the get_field and set_field methods.
Writes out the PDL, sets datatype and dimensions automatically, overwriting your own values, take care!
$nii->set_field(<name>,<value>,[pos]); Sets field <name> to <value>. If the field is an array, <value> is interpreted as an array reference, unless pos is supplied.
$par=$nii->get_field(<name>,[pos]); returns header values, same rules regarding arrays as in set_field applay.
so far only used/tested internally, but may be useful. They pack and write or retrieve and unpack the header, respectively.
At the moment, read_nii only of native PDL datatypes have been tested.
I guess a lot, this is the first alpha. It needs a lot of testing, still.
http://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h - the Nifti standard on which this module is based.
Albrecht Ingo Schmid