Saturday, January 31, 2015

Using pynrrd to read nrrd files into Python

Another in the series of posts about file types! This time, a quick note about importing .nrrd image stacks into Python. Download and unzip pynrrd from here. In a terminal, cd into the directory, and run

python setup.py install

In Python the usage is very straightforward:

import nrrd
frames, options = nrrd.read(fileName)


2 comments:

lana frankle said...

I'm getting the following error:

TypeError: coercing to Unicode: need string or buffer, module found

Can you help me? I entered:

frames, options = nrrd.read(nrrd)

Peter Weir said...

Hi Lana,

In order to read a file named 'filename.nrrd' you need to navigate to the directory the file is in, then enter:

import nrrd
frames, options = nrrd.read('filename.nrrd')

Note that in your case you gave the same variable name, nrrd, to both the module you imported and the file name you are trying to open.