quick ecat to nifti

ecat2nii.py

#! /usr/bin/env python
import sys, os
import nibabel as ni
import nibabel.ecat as ecat
import numpy as np

def print_smoothed(infile):
    """ prints smoothing kernel FWHM for each file to stdout"""
    try:
        img = ecat.load(infile)
        shdrs = img.get_subheaders()
        fwhm = shdrs.subheaders[0]['rfilter_resolution'].item() * 10
        print 'smoothed(%2.2f):'%fwhm
    except:
        print 'Error reading file %s'%infile

def print_header(infile):
    """ prints header data for infile to std out"""

    try:
        img = ecat.load(infile)
        hdr = img.get_header()
        for k,v in hdr.items():
            print k,v
    except:
        print 'Error reading file %s'%infile

def get_framenumbers(infile, frame=0):
    """ Returns the order of the frames in the file
    Useful as sometimes Frames are not stored in the file in
    chronological order, and can be used to extract frames
    in correct order

    returns
    frameorder_in_file : [true_framenumber, mlist_id]
    """
    img = ecat.load(infile)
    mlist = img.get_mlist()
    realframes = mlist.get_frame_order()
    len_mlist = mlist._mlist[mlist._mlist[:,0] > 0].shape[0]
    hdr = img.get_header()
    nframes = hdr['num_frames']
    realframe = frame #realframes[frame][0]
    framenumbers = np.arange(nframes - len_mlist, nframes)

    if len(framenumbers) ==1:
        return framenumbers[0]
    else:
        return framenumbers[realframe]

def check_dtypes(infile):
    frame_numbers = get_framenumbers(infile)
    img = ecat.load(infile)
    shdrs = img.get_subheaders()
    # get data_type
    dtypes = [x['data_type'].item() for x in shdrs.subheaders]
    if not all([x == dtypes[0] for x in dtypes]):
        raise StandardError('warning: data frames have different datatypes')
    if dtypes[0] == 6:
        return np.uint16
    elif dtypes[0] == 5:
        return np.float
    else:
        raise StandardError( 'Unknown datatype code %s'%dtypes[0])

def convert2nifti(img, frame = 0, dtype=None):
    if dtype:
        tmpimg = ni.Nifti1Image(img.get_frame(frame,
                                              orientation='neurological'
                                              ).astype(dtype),
                                img.get_frame_affine(frame))
    else:
        tmpimg = ni.Nifti1Image(img.get_frame(frame,
                                              orientation='neurological',
                                              ),
                                img.get_frame_affine(frame))
    return tmpimg

def save_file(image, filename):
    """ saves image to filename"""
    image.to_filename(filename)

def create_outfile(infile, inimg, frame, newname=None):

    pth, nme_ext = os.path.split(infile)

    if inimg.__class__ == ni.Nifti1Image:
        ext = '.nii'
    else:
        raise IOError('Unknown Image format %s,unable to save'%(infile.__class__))
    if newname is None:
        newname = os.path.splitext(nme_ext)[0]

    correct_frame_number = get_framenumbers(infile, frame)

    outname = newname + '_frame%04d'%(correct_frame_number + 1) + ext
    outfile = os.path.join(pth, outname)
    return outfile

if __name__ == '__main__':

    try:
        infile = sys.argv[1]
    except:
        raise IOError('Please pass file to convert')

    eimg = ecat.load(infile)
    mlist = eimg.get_mlist()
    nframes = mlist.get_frame_order()
    for realframe, index in nframes.items():
        print 'rf,', realframe, 'index', index[0]
        niimg = convert2nifti(eimg, index[0])
        outf = create_outfile(infile, niimg, realframe)
        niimg.to_filename(outf)
        print outf

Hm... I'm trying this and it isn't working for me. I'm wondering if I'm perhaps rolling a newer version of nibabel?

It looks like img.get_mlist() returns an ndarray now, so it doesn't have attributes like _mlist and or get_frame_order(). I think I can make it go; if so I'll try and post an update.