ENH: Remove img.get_data() from internal use

nibabel/__init__.py

@@ -23,7 +23,7 @@
    img2 = nib.load('other_file.nii.gz')
    img3 = nib.load('spm_file.img')
 
-   data = img1.get_data()
+   data = img1.get_fdata()
    affine = img1.affine
 
    print(img1)

nibabel/analyze.py

@@ -1009,7 +1009,7 @@ def to_file_map(self, file_map=None):
         '''
         if file_map is None:
             file_map = self.file_map
-        data = self.get_data()
+        data = np.asanyarray(self.dataobj)
         self.update_header()
         hdr = self._header
         out_dtype = self.get_data_dtype()

nibabel/brikhead.py

@@ -486,7 +486,7 @@ class AFNIImage(SpatialImage):
            [  0.    ,   0.    ,   3.    , -52.3511],
            [  0.    ,   0.    ,   0.    ,   1.    ]])
     >>> head = load(os.path.join(datadir, 'example4d+orig.HEAD'))
-    >>> np.array_equal(head.get_data(), brik.get_data())
+    >>> np.array_equal(head.get_fdata(), brik.get_fdata())
     True
     """
 

nibabel/cifti2/tests/test_cifti2io_axes.py

@@ -93,8 +93,8 @@ def check_rewrite(arr, axes, extension='.nii'):
     (fd, name) = tempfile.mkstemp(extension)
     cifti2.Cifti2Image(arr, header=axes).to_filename(name)
     img = nib.load(name)
-    arr2 = img.get_data()
-    assert (arr == arr2).all()
+    arr2 = img.get_fdata()
+    assert np.allclose(arr, arr2)
     for idx in range(len(img.shape)):
         assert (axes[idx] == img.header.get_axis(idx))
     return img
@@ -103,7 +103,7 @@ def check_rewrite(arr, axes, extension='.nii'):
 @needs_nibabel_data('nitest-cifti2')
 def test_read_ones():
     img = nib.load(os.path.join(test_directory, 'ones.dscalar.nii'))
-    arr = img.get_data()
+    arr = img.get_fdata()
     axes = [img.header.get_axis(dim) for dim in range(2)]
     assert (arr == 1).all()
     assert isinstance(axes[0], cifti2_axes.ScalarAxis)
@@ -118,7 +118,7 @@ def test_read_ones():
 @needs_nibabel_data('nitest-cifti2')
 def test_read_conte69_dscalar():
     img = nib.load(os.path.join(test_directory, 'Conte69.MyelinAndCorrThickness.32k_fs_LR.dscalar.nii'))
-    arr = img.get_data()
+    arr = img.get_fdata()
     axes = [img.header.get_axis(dim) for dim in range(2)]
     assert isinstance(axes[0], cifti2_axes.ScalarAxis)
     assert len(axes[0]) == 2
@@ -132,7 +132,7 @@ def test_read_conte69_dscalar():
 @needs_nibabel_data('nitest-cifti2')
 def test_read_conte69_dtseries():
     img = nib.load(os.path.join(test_directory, 'Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii'))
-    arr = img.get_data()
+    arr = img.get_fdata()
     axes = [img.header.get_axis(dim) for dim in range(2)]
     assert isinstance(axes[0], cifti2_axes.SeriesAxis)
     assert len(axes[0]) == 2
@@ -147,7 +147,7 @@ def test_read_conte69_dtseries():
 @needs_nibabel_data('nitest-cifti2')
 def test_read_conte69_dlabel():
     img = nib.load(os.path.join(test_directory, 'Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii'))
-    arr = img.get_data()
+    arr = img.get_fdata()
     axes = [img.header.get_axis(dim) for dim in range(2)]
     assert isinstance(axes[0], cifti2_axes.LabelAxis)
     assert len(axes[0]) == 3
@@ -162,7 +162,7 @@ def test_read_conte69_dlabel():
 @needs_nibabel_data('nitest-cifti2')
 def test_read_conte69_ptseries():
     img = nib.load(os.path.join(test_directory, 'Conte69.MyelinAndCorrThickness.32k_fs_LR.ptseries.nii'))
-    arr = img.get_data()
+    arr = img.get_fdata()
     axes = [img.header.get_axis(dim) for dim in range(2)]
     assert isinstance(axes[0], cifti2_axes.SeriesAxis)
     assert len(axes[0]) == 2

nibabel/cifti2/tests/test_cifti2io_header.py

@@ -63,11 +63,11 @@ def test_read_and_proxies():
     assert_equal(img2.shape, (1, 91282))
     # While we cannot reshape arrayproxies, all images are in-memory
     assert_true(not img2.in_memory)
-    data = img2.get_data()
+    data = img2.get_fdata()
     assert_true(data is not img2.dataobj)
     # Uncaching has no effect, images are always array images
     img2.uncache()
-    assert_true(data is not img2.get_data())
+    assert_true(data is not img2.get_fdata())
 
 
 @needs_nibabel_data('nitest-cifti2')

nibabel/cifti2/tests/test_new_cifti2.py

@@ -13,7 +13,8 @@
 from nibabel.tmpdirs import InTemporaryDirectory
 
 from nose.tools import assert_true, assert_equal, assert_raises
-from nibabel.testing import clear_and_catch_warnings, error_warnings, suppress_warnings
+from nibabel.testing import (
+    clear_and_catch_warnings, error_warnings, suppress_warnings, assert_array_equal)
 
 affine = [[-1.5, 0, 0, 90],
           [0, 1.5, 0, -85],
@@ -246,7 +247,7 @@ def test_dtseries():
         assert_equal(img2.nifti_header.get_intent()[0],
                      'ConnDenseSeries')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         check_series_map(img2.header.matrix.get_index_map(0))
         check_geometry_map(img2.header.matrix.get_index_map(1))
         del img2
@@ -268,7 +269,7 @@ def test_dscalar():
         img2 = nib.load('test.dscalar.nii')
         assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseScalar')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         check_scalar_map(img2.header.matrix.get_index_map(0))
         check_geometry_map(img2.header.matrix.get_index_map(1))
         del img2
@@ -290,7 +291,7 @@ def test_dlabel():
         img2 = nib.load('test.dlabel.nii')
         assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseLabel')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         check_label_map(img2.header.matrix.get_index_map(0))
         check_geometry_map(img2.header.matrix.get_index_map(1))
         del img2
@@ -310,7 +311,7 @@ def test_dconn():
         img2 = nib.load('test.dconn.nii')
         assert_equal(img2.nifti_header.get_intent()[0], 'ConnDense')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         assert_equal(img2.header.matrix.get_index_map(0),
                      img2.header.matrix.get_index_map(1))
         check_geometry_map(img2.header.matrix.get_index_map(0))
@@ -333,7 +334,7 @@ def test_ptseries():
         img2 = nib.load('test.ptseries.nii')
         assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelSries')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         check_series_map(img2.header.matrix.get_index_map(0))
         check_parcel_map(img2.header.matrix.get_index_map(1))
         del img2
@@ -355,7 +356,7 @@ def test_pscalar():
         img2 = nib.load('test.pscalar.nii')
         assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelScalr')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         check_scalar_map(img2.header.matrix.get_index_map(0))
         check_parcel_map(img2.header.matrix.get_index_map(1))
         del img2
@@ -377,7 +378,7 @@ def test_pdconn():
         img2 = ci.load('test.pdconn.nii')
         assert_equal(img2.nifti_header.get_intent()[0], 'ConnParcelDense')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         check_geometry_map(img2.header.matrix.get_index_map(0))
         check_parcel_map(img2.header.matrix.get_index_map(1))
         del img2
@@ -399,7 +400,7 @@ def test_dpconn():
         img2 = ci.load('test.dpconn.nii')
         assert_equal(img2.nifti_header.get_intent()[0], 'ConnDenseParcel')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         check_parcel_map(img2.header.matrix.get_index_map(0))
         check_geometry_map(img2.header.matrix.get_index_map(1))
         del img2
@@ -420,7 +421,7 @@ def test_plabel():
         img2 = ci.load('test.plabel.nii')
         assert_equal(img.nifti_header.get_intent()[0], 'ConnUnknown')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         check_label_map(img2.header.matrix.get_index_map(0))
         check_parcel_map(img2.header.matrix.get_index_map(1))
         del img2
@@ -440,7 +441,7 @@ def test_pconn():
         img2 = ci.load('test.pconn.nii')
         assert_equal(img.nifti_header.get_intent()[0], 'ConnParcels')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         assert_equal(img2.header.matrix.get_index_map(0),
                      img2.header.matrix.get_index_map(1))
         check_parcel_map(img2.header.matrix.get_index_map(0))
@@ -465,7 +466,7 @@ def test_pconnseries():
         img2 = ci.load('test.pconnseries.nii')
         assert_equal(img.nifti_header.get_intent()[0], 'ConnPPSr')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         assert_equal(img2.header.matrix.get_index_map(0),
                      img2.header.matrix.get_index_map(1))
         check_parcel_map(img2.header.matrix.get_index_map(0))
@@ -491,7 +492,7 @@ def test_pconnscalar():
         img2 = ci.load('test.pconnscalar.nii')
         assert_equal(img.nifti_header.get_intent()[0], 'ConnPPSc')
         assert_true(isinstance(img2, ci.Cifti2Image))
-        assert_true((img2.get_data() == data).all())
+        assert_array_equal(img2.get_fdata(), data)
         assert_equal(img2.header.matrix.get_index_map(0),
                      img2.header.matrix.get_index_map(1))
 

nibabel/cmdline/ls.py

@@ -125,7 +125,7 @@ def proc_file(f, opts):
     if opts.stats or opts.counts:
         # We are doomed to load data
         try:
-            d = vol.get_data()
+            d = np.asarray(vol.dataobj)
             if not opts.stats_zeros:
                 d = d[np.nonzero(d)]
             else:

nibabel/dataobj_images.py

@@ -68,8 +68,8 @@ def get_data(self, caching='fill'):
 
             We recommend you use the ``get_fdata`` method instead of the
             ``get_data`` method, because it is easier to predict the return
-            data type.  We will deprecate the ``get_data`` method around April
-            2018, and remove it around April 2020.
+            data type.  ``get_data`` will be deprecated around November 2019
+            and removed around November 2021.
 
             If you don't care about the predictability of the return data type,
             and you want the minimum possible data size in memory, you can

nibabel/ecat.py

@@ -788,7 +788,7 @@ def __init__(self, dataobj, affine, header,
         >>> frame0 = img.get_frame(0)
         >>> frame0.shape == (10, 10, 3)
         True
-        >>> data4d = img.get_data()
+        >>> data4d = img.get_fdata()
         >>> data4d.shape == (10, 10, 3, 1)
         True
         """
@@ -945,7 +945,7 @@ def to_file_map(self, file_map=None):
 
         # It appears to be necessary to load the data before saving even if the
         # data itself is not used.
-        self.get_data()
+        self.get_fdata()
         hdr = self.header
         mlist = self._mlist
         subheaders = self.get_subheaders()

nibabel/filebasedimages.py

@@ -120,7 +120,7 @@ class FileBasedImage(object):
 
     You can get the data out again with::
 
-        img.get_data()
+        img.get_fdata()
 
     Less commonly, for some image types that support it, you might want to
     fetch out the unscaled array via the object containing the data::

nibabel/freesurfer/mghformat.py

@@ -594,7 +594,7 @@ def to_file_map(self, file_map=None):
         '''
         if file_map is None:
             file_map = self.file_map
-        data = self.get_data()
+        data = np.asanyarray(self.dataobj)
         self.update_header()
         hdr = self.header
         with file_map['image'].get_prepare_fileobj('wb') as mghf:

nibabel/freesurfer/tests/test_mghformat.py

@@ -81,7 +81,7 @@ def test_read_mgh():
     assert_array_almost_equal(h.get_vox2ras_tkr(), v2rtkr)
 
     # data. will be different for your own mri_volsynth invocation
-    v = mgz.get_data()
+    v = mgz.get_fdata()
     assert_almost_equal(v[1, 2, 3, 0], -0.3047, 4)
     assert_almost_equal(v[1, 2, 3, 1], 0.0018, 4)
 
@@ -97,7 +97,7 @@ def test_write_mgh():
         # read from the tmp file and see if it checks out
         mgz = load('tmpsave.mgz')
         h = mgz.header
-        dat = mgz.get_data()
+        dat = mgz.get_fdata()
         # Delete loaded image to allow file deletion by windows
         del mgz
     # header
@@ -193,7 +193,7 @@ def test_filename_exts():
             save(img, fname)
             # read from the tmp file and see if it checks out
             img_back = load(fname)
-            assert_array_equal(img_back.get_data(), v)
+            assert_array_equal(img_back.get_fdata(), v)
             del img_back
 
 
@@ -288,7 +288,7 @@ def test_mgh_load_fileobj():
     fm = MGHImage.make_file_map(mapping=dict(image=bio))
     img2 = MGHImage.from_file_map(fm)
     assert_true(img2.dataobj.file_like is bio)
-    assert_array_equal(img.get_data(), img2.get_data())
+    assert_array_equal(img.get_fdata(), img2.get_fdata())
 
 
 def test_mgh_affine_default():

nibabel/funcs.py

@@ -79,8 +79,7 @@ def squeeze_image(img):
     if slen == len(shape):
         return klass.from_image(img)
     shape = shape[:slen]
-    data = img.get_data()
-    data = data.reshape(shape)
+    data = np.asanyarray(img.dataobj).reshape(shape)
     return klass(data,
                  img.affine,
                  img.header,
@@ -144,7 +143,7 @@ def concat_images(images, check_affines=True, axis=None):
             raise ValueError('Affine for image {0} does not match affine '
                              'for first image'.format(i))
         # Do not fill cache in image if it is empty
-        out_data[i] = img.get_data(caching='unchanged')
+        out_data[i] = np.asanyarray(img.dataobj)
 
     if axis is None:
         out_data = np.rollaxis(out_data, 0, out_data.ndim)
@@ -169,7 +168,7 @@ def four_to_three(img):
     imgs : list
        list of 3D images
     '''
-    arr = img.get_data()
+    arr = np.asanyarray(img.dataobj)
     header = img.header
     affine = img.affine
     image_maker = img.__class__

nibabel/loadsave.py

@@ -155,7 +155,7 @@ def read_img_data(img, prefer='scaled'):
     """ Read data from image associated with files
 
     If you want unscaled data, please use ``img.dataobj.get_unscaled()``
-    instead.  If you want scaled data, use ``img.get_data()`` (which will cache
+    instead.  If you want scaled data, use ``img.get_fdata()`` (which will cache
     the loaded array) or ``np.array(img.dataobj)`` (which won't cache the
     array). If you want to load the data as for a modified header, save the
     image with the modified header, and reload.
@@ -164,7 +164,7 @@ def read_img_data(img, prefer='scaled'):
     ----------
     img : ``SpatialImage``
        Image with valid image file in ``img.file_map``.  Unlike the
-       ``img.get_data()`` method, this function returns the data read
+       ``img.get_fdata()`` method, this function returns the data read
        from the image file, as specified by the *current* image header
        and *current* image files.
     prefer : str, optional

nibabel/minc2.py

@@ -16,7 +16,7 @@
 
     import nibabel as nib
     img = nib.load('my_funny.mnc')
-    data = img.get_data()
+    data = img.get_fdata()
     print(data.mean())
     print(data.max())
     print(data.min())

nibabel/processing.py

@@ -233,7 +233,7 @@ def resample_to_output(in_img,
     # looks like when resampled into world coordinates
     if n_dim < 3:  # Expand image to 3D, make voxel sizes match
         new_shape = in_shape + (1,) * (3 - n_dim)
-        data = in_img.get_data().reshape(new_shape)  # 2D data should be small
+        data = np.asanyarray(in_img.dataobj).reshape(new_shape)  # 2D data should be small
         in_img = out_class(data, in_img.affine, in_img.header)
         if voxel_sizes is not None and len(voxel_sizes) == n_dim:
             # Need to pad out voxel sizes to match new image dimensions

nibabel/spaces.py

@@ -112,7 +112,7 @@ def slice2volume(index, axis, shape=None):
     and then use ``whole_aff`` in ``scipy.ndimage.affine_transform``:
 
         rzs, trans = to_matvec(whole_aff)
-        data = img2.get_data()
+        data = img2.get_fdata()
         new_slice = scipy.ndimage.affine_transform(data, rzs, trans, slice_shape)
 
     Parameters