Merge pull request #82 from schwarty/master

concat_images can use filenames or images

Author: matthew-brett

nibabel/funcs.py

@@ -1,3 +1,4 @@
+
 # emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
@@ -11,6 +12,7 @@
 
 from .orientations import (io_orientation, orientation_affine, flip_axis,
                            apply_orientation, OrientationError)
+from .loadsave import load
 
 
 def squeeze_image(img):
@@ -92,7 +94,7 @@ def concat_images(images, check_affines=True):
     Parameters
     ----------
     images : sequence
-       sequence of ``SpatialImage``\s
+       sequence of ``SpatialImage`` or of filenames\s
     check_affines : {True, False}, optional
        If True, then check that all the affines for `images` are nearly
        the same, raising a ``ValueError`` otherwise.  Default is True
@@ -105,12 +107,18 @@ def concat_images(images, check_affines=True):
     '''
     n_imgs = len(images)
     img0 = images[0]
+    is_filename = False
+    if not hasattr(img0, 'get_data'):
+        img0 = load(img0)
+        is_filename = True
     i0shape = img0.shape
     affine = img0.get_affine()
     header = img0.get_header()
     out_shape = (n_imgs, ) + i0shape
     out_data = np.empty(out_shape)
     for i, img in enumerate(images):
+        if is_filename:
+            img = load(img)
         if check_affines:
             if not np.all(img.get_affine() == affine):
                 raise ValueError('Affines do not match')

nibabel/tests/test_funcs.py

@@ -8,15 +8,17 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 ''' Test for image funcs '''
 
+import os
+import tempfile
 import numpy as np
 
 from ..funcs import concat_images, as_closest_canonical, OrientationError
 from ..nifti1 import Nifti1Image
+from ..loadsave import save
 
 from numpy.testing import assert_array_equal
 from nose.tools import (assert_true, assert_false, assert_equal, assert_raises)
 
-
 def test_concat():
     shape = (1,2,5)
     data0 = np.arange(10).reshape(shape)
@@ -40,6 +42,35 @@ def test_concat():
     assert_array_equal(all_imgs.get_affine(), affine)
 
 
+def test_concat_with_filenames():
+    shape = (1,2,5)
+    data0 = np.arange(10).reshape(shape)
+    affine = np.eye(4)
+    img0 = Nifti1Image(data0, affine)
+    img0_path = tempfile.mkstemp(suffix='.nii')[1]
+    save(img0, img0_path)
+    data1 = data0 - 10
+    img1 = Nifti1Image(data1, affine)
+    img1_path = tempfile.mkstemp(suffix='.nii')[1]
+    save(img1, img1_path)
+    all_imgs = concat_images([img0_path, img1_path])
+    all_data = np.concatenate(
+        [data0[:,:,:,np.newaxis],data1[:,:,:,np.newaxis]],3)
+    assert_array_equal(all_imgs.get_data(), all_data)
+    assert_array_equal(all_imgs.get_affine(), affine)
+    # check that not-matching affines raise error
+    img2 = Nifti1Image(data1, affine+1)
+    assert_raises(ValueError, concat_images, [img0, img2])
+    img2 = Nifti1Image(data1.T, affine)
+    assert_raises(ValueError, concat_images, [img0, img2])
+    # except if check_affines is False
+    all_imgs = concat_images([img0, img1])
+    assert_array_equal(all_imgs.get_data(), all_data)
+    assert_array_equal(all_imgs.get_affine(), affine)
+    os.remove(img0_path)
+    os.remove(img1_path)
+
+
 def test_closest_canonical():
     arr = np.arange(24).reshape((2,3,4,1))
     # no funky stuff, returns same thing