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PYTHON_2TO3.md

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List of changes to upgrade code from Python 2.7 to 3.8

Installation

The outsource python packages has been updated as to be compatible with the new Python 3.8 interpreter:

  • Graph-tool: installed with conda, version 2.29, newer versions fails for Python 3.8 (24/08/2020).
  • beautifulsoup4, lxml, numpy, opencv, pillow, scikit-image, scikit-learn, vtk, scikit-fmm, pytest: latest version installed with conda.
  • astropy: installed with ??, to substitute the deprecated PyFITS TODO.
  • imageio: new in Python 3, to substitue scipy.misc.{imread,imsave}

Code modifications

Most of the job is done by the script 2to3 provided in Python 3. However, some additional modifications were required, they are listed below.

Syntaxis

  • In literals is and is not is substituted by == and != respectively.

Pickling

  • Unpickling:
    f_pkl = open(fname, 'rb') # Instead of just open(fname)
    try:
        gen_obj = pickle.load(f_pkl)
    finally:
        f_pkl.close()

I/O for PNG images

Scipy I/O functions are no longer available for Python 3, now the functions:

from imageio import imread, imwrite
# from scipy.misc import imsave, imread # For Python 2.7
...
# imsave is susbtituted by imread for all functions called

To allow 16 bits graylevel precision without loss for PNG images, the image data mapping to uint16 type, usually from float, has to be done explicitly before the call imwrite function:

imwrite(part_name, lin_map(self.__particles[count],0,np.iinfo(np.uint16).max).astype(np.uint16))

I/O for FITS image

Package pyfits is deprecated for Python 3, now it is include in the package astropy, that required the next chnages:

from astropy.io import fits
# import pyfits # For Python 2.7
...
fits.writeto(fname, array, overwrite=True, output_verify='silentfix')
# pyfits.writeto(fname, array, overwrite=True, output_verify='silentfix') # For Python 2.7
...
hold = fits.getdata(DATA_DIR + '/mb_seg.fits')
# hold = pyfits.getdata(DATA_DIR + '/mb_seg.fits') # For Python 2.7

Multiprocessing

In calls to Array function to create shared arrays as input parameter to size_or_initializer on accepts type int (e.g. int64 raises errors), for that reason a explicit cast before the function call may be necessary:

# particles_sh, masks_sh = mp.Array('f', part_h*part_r*npart), mp.Array('f', part_h*part_r*npart) # Python 2.7
particles_sh, masks_sh = mp.Array('f', int(part_h*part_r*npart)), mp.Array('f', int(part_h*part_r*npart))

Pyto

In function geometry.affine.transformArray the old input paramter origin is now called center.

# particle = r3d.transformArray(particle_u, origin=svol_cent, order=3, prefilter=True) # Python 2.7
particle = r3d.transformArray(particle_u, center=svol_cent, order=3, prefilter=True)

Scikit-fmm

Because some unhandled and recently discovered numerical errors, scikit-fmm version=2019.1.30), the function skfmm.travel_time() is substitued by skfmm.distance():

dst_field = np.ma.MaskedArray(dst_field, np.invert(self.__voi))
self.__dst_field = skfmm.distance(dst_field, dx=1) 
# skfmm.travel_time(dst_field, self.__voi.astype(np.float32), dx=1) # Python 2.7

Catching exceptions

The syntax has changed for catching several exceptions at once:

except (ValueError, IndexError):
# except ValueError, IndexError: # Python 2.7