io casting

ants/core/ants_image_io.py

@@ -18,6 +18,7 @@
 import os
 import json
 import numpy as np
+import warnings
 
 from . import ants_image as iio
 from .. import utils
@@ -401,7 +402,8 @@ def image_read(filename, dimension=None, pixeltype='float'):
             ndim = dimension
 
         if ptype in _unsupported_ptypes:
-            raise ValueError('unsupported pixeltype %s' % ptype)
+            #warnings.warn('Casting image from unsupported type \'%s\' to closest supported type \'%s\'' % (ptype, _unsupported_ptype_map[ptype]))
+            ptype = _unsupported_ptype_map.get(ptype, 'unsupported')
 
         libfn = utils.get_lib_fn(_image_read_dict[pclass][ptype][ndim])
         itk_pointer = libfn(filename)

ants/viz/plot.py

@@ -195,7 +195,7 @@ def plot(image, overlay=None, cmap='Greys_r', overlay_cmap='jet', overlay_alpha=
 
 
 def plot_directory(directory, recursive=False, regex='*', 
-                   save_prefix='', save_suffix='', **kwargs):
+                   save_prefix='', save_suffix='', axis=None, **kwargs):
     """
     Create and save an ANTsPy plot for every image matching a given regular
     expression in a directory, optionally recursively. This is a good function
@@ -254,8 +254,14 @@ def has_acceptable_suffix(fname):
                 fname = '%s%s' % (save_prefix, fname)
                 save_fname = os.path.join(root, fname)
                 img = iio2.image_read(load_fname)
+
+                if axis is None:
+                    axis_range = [i for i in range(img.dimension)]
+                else:
+                    axis_range = axis if isinstance(axis,(list,tuple)) else [axis]
+
                 if img.dimension > 2:
-                    for axis_idx in range(img.dimension):
+                    for axis_idx in axis_range:
                         filename = save_fname.replace('.png', '_axis%i.png' % axis_idx)
                         ncol = int(math.sqrt(img.shape[axis_idx]))
                         plot(img, axis=axis_idx, nslices=img.shape[axis_idx], ncol=ncol,

tests/timings_io.py

@@ -41,7 +41,7 @@ def test_itk():
 
     def test_ants():
         for img_path in img_paths:
-            array = ants.image_read(img_path).numpy()
+            array = ants.image_read(img_path, pixeltype='float').numpy()
 
     nib_start = time.time()
     for i in range(N_TRIALS):