[DATALAD RUNCMD] RF: .get_shape() -> .shape to address nibabel deprecation

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "git-sedi '\\.get_shape()' .shape",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [
  "doc",
  "src",
  "test"
 ],
 "pwd": "."
}
^^^ Do not change lines above ^^^

Author: yarikoptic

doc/Python_Tutorial.rst

@@ -150,25 +150,25 @@ method *split*.
     >>> from dcmstack.dcmmeta import NiftiWrapper
     >>> nw1 = NiftiWrapper.from_filename('img1.nii.gz')
     >>> nw2 = NiftiWrapper.from_filename('img2.nii.gz')
-    >>> print nw1.nii_img.get_shape()
+    >>> print nw1.nii_img.shape
     (384, 512, 60)
-    >>> print nw2.nii_img.get_shape()
+    >>> print nw2.nii_img.shape
     (384, 512, 60)
     >>> print nw1.get_meta('EchoTime')
     11.0
     >>> print nw2.get_meta('EchoTime')
     87.0
     >>> merged = NiftiWrapper.from_sequence([nw1, nw2])
-    >>> print merged.nii_img.get_shape()
+    >>> print merged.nii_img.shape
     (384, 512, 60, 2)
     >>> print merged.get_meta('EchoTime', index=(0,0,0,0)
     11.0
     >>> print merged.get_meta('EchoTime', index=(0,0,0,1)
     87.0
     >>> splits = list(merge.split())
-    >>> print splits[0].nii_img.get_shape()
+    >>> print splits[0].nii_img.shape
     (384, 512, 60)
-    >>> print splits[1].nii_img.get_shape()
+    >>> print splits[1].nii_img.shape
     (384, 512, 60)
     >>> print splits[0].get_meta('EchoTime')
     11.0

src/dcmstack/dcmmeta.py

@@ -1292,7 +1292,7 @@ def meta_valid(self, classification):
         if classification == ('global', 'const'):
             return True
 
-        img_shape = self.nii_img.get_shape()
+        img_shape = self.nii_img.shape
         meta_shape = self.meta_ext.shape
         if classification == ('vector', 'samples'):
             return meta_shape[4:] == img_shape[4:]
@@ -1357,7 +1357,7 @@ def get_meta(self, key, index=None, default=None):
         #If an index is provided check the varying values
         if not index is None:
             #Test if the index is valid
-            shape = self.nii_img.get_shape()
+            shape = self.nii_img.shape
             if len(index) != len(shape):
                 raise IndexError('Incorrect number of indices.')
             for dim, ind_val in enumerate(index):
@@ -1434,7 +1434,7 @@ def split(self, dim=None):
             along `dim`.
 
         '''
-        shape = self.nii_img.get_shape()
+        shape = self.nii_img.shape
         data = self.nii_img.get_data()
         header = self.nii_img.header
         slice_dim = header.get_dim_info()[2]

src/dcmstack/dcmstack.py

@@ -750,7 +750,7 @@ def get_shape(self):
                             num_vec_comps)
 
         #Stack appears to be valid, build the shape tuple
-        file_shape = self._files_info[0][0].nii_img.get_shape()
+        file_shape = self._files_info[0][0].nii_img.shape
         vol_shape = list(file_shape)
         if files_per_vol > 1:
             vol_shape[2] = files_per_vol
@@ -777,7 +777,7 @@ def get_data(self):
             The stack is incomplete or invalid.
         '''
         #Create a numpy array for storing the voxel data
-        stack_shape = self.get_shape()
+        stack_shape = self.shape
         stack_shape = tuple(list(stack_shape) + ((5 - len(stack_shape)) * [1]))
         stack_dtype = self._files_info[0][0].nii_img.get_data_dtype()
         bits_stored = self._files_info[0][0].get_meta('BitsStored', default=16)
@@ -795,7 +795,7 @@ def get_data(self):
         if len(stack_shape) > 4:
             n_vols *= stack_shape[4]
         files_per_vol = len(self._files_info) // n_vols
-        file_shape = self._files_info[0][0].nii_img.get_shape()
+        file_shape = self._files_info[0][0].nii_img.shape
         for vec_idx in range(stack_shape[4]):
             for time_idx in range(stack_shape[3]):
                 if files_per_vol == 1 and file_shape[2] != 1:
@@ -831,7 +831,7 @@ def get_affine(self):
             The stack is incomplete or invalid.
         '''
         #Figure out the number of three (or two) dimensional volumes
-        shape = self.get_shape()
+        shape = self.shape
         n_vols = 1
         if len(shape) > 3:
             n_vols *= shape[3]

test/test_dcmmeta.py

@@ -1142,7 +1142,7 @@ def test_from_dicom():
     meta = {'EchoTime': 40}
     nw = dcmmeta.NiftiWrapper.from_dicom(src_dcm, meta)
     hdr = nw.nii_img.header
-    eq_(nw.nii_img.get_shape(), (192, 192, 1))
+    eq_(nw.nii_img.shape, (192, 192, 1))
     ok_(np.allclose(np.dot(np.diag([-1., -1., 1., 1.]), src_dw.get_affine()),
                     nw.nii_img.get_affine())
        )

test/test_dcmstack.py

@@ -365,14 +365,14 @@ def setUp(self):
     def test_single_slice(self):
         stack = dcmstack.DicomStack()
         stack.add_dcm(self.inputs[0])
-        shape = stack.get_shape()
+        shape = stack.shape
         eq_(shape, (192, 192, 1))
 
     def test_three_dim(self):
         stack = dcmstack.DicomStack()
         stack.add_dcm(self.inputs[0])
         stack.add_dcm(self.inputs[1])
-        shape = stack.get_shape()
+        shape = stack.shape
         eq_(shape, (192, 192, 2))
 
     def test_four_dim(self):
@@ -381,7 +381,7 @@ def test_four_dim(self):
         stack.add_dcm(self.inputs[1])
         stack.add_dcm(self.inputs[2])
         stack.add_dcm(self.inputs[3])
-        shape = stack.get_shape()
+        shape = stack.shape
         eq_(shape, (192, 192, 2, 2))
 
     def test_five_dim(self):
@@ -390,7 +390,7 @@ def test_five_dim(self):
         stack.add_dcm(self.inputs[1])
         stack.add_dcm(self.inputs[2])
         stack.add_dcm(self.inputs[3])
-        shape = stack.get_shape()
+        shape = stack.shape
         eq_(shape, (192, 192, 2, 1, 2))
 
     def test_allow_dummy(self):
@@ -399,7 +399,7 @@ def test_allow_dummy(self):
         stack = dcmstack.DicomStack(allow_dummies=True)
         stack.add_dcm(self.inputs[0])
         stack.add_dcm(self.inputs[1])
-        shape = stack.get_shape()
+        shape = stack.shape
         eq_(shape, (192, 192, 2))
 
 class TestGuessDim(object):
@@ -435,7 +435,7 @@ def test_single_guess(self):
             for idx, in_dcm in enumerate(self.inputs):
                 setattr(in_dcm, key, self._get_vr_ord(key, idx))
                 stack.add_dcm(in_dcm)
-            eq_(stack.get_shape(), (192, 192, 2, 2))
+            eq_(stack.shape, (192, 192, 2, 2))
             for in_dcm in self.inputs:
                 delattr(in_dcm, key)
 
@@ -450,7 +450,7 @@ def test_wrong_guess_first(self):
                     dcmstack.DicomStack.sort_guesses[-1],
                     self._get_vr_ord(key, idx) )
             stack.add_dcm(in_dcm)
-        eq_(stack.get_shape(), (192, 192, 2, 2))
+        eq_(stack.shape, (192, 192, 2, 2))
 
 class TestGetData(object):
     def setUp(self):
@@ -470,7 +470,7 @@ def test_single_slice(self):
         stack = dcmstack.DicomStack()
         stack.add_dcm(self.inputs[0])
         data = stack.get_data()
-        eq_(data.shape, stack.get_shape())
+        eq_(data.shape, stack.shape)
         eq_(sha256(data).hexdigest(),
             '15cfa107ca73810a1c97f1c1872a7a4a05808ba6147e039cef3f63fa08735f5d')
 
@@ -479,7 +479,7 @@ def test_three_dim(self):
         stack.add_dcm(self.inputs[0])
         stack.add_dcm(self.inputs[1])
         data = stack.get_data()
-        eq_(data.shape, stack.get_shape())
+        eq_(data.shape, stack.shape)
         eq_(sha256(data).hexdigest(),
             'ab5225fdbedceeea3442b2c9387e1abcbf398c71f525e0017251849c3cfbf49c')
 
@@ -490,7 +490,7 @@ def test_four_dim(self):
         stack.add_dcm(self.inputs[2])
         stack.add_dcm(self.inputs[3])
         data = stack.get_data()
-        eq_(data.shape, stack.get_shape())
+        eq_(data.shape, stack.shape)
         eq_(sha256(data).hexdigest(),
             'bb3639a6ece13dc9a11d65f1b09ab3ccaed63b22dcf0f96fb5d3dd8805cc7b8a')
 
@@ -501,7 +501,7 @@ def test_five_dim(self):
         stack.add_dcm(self.inputs[2])
         stack.add_dcm(self.inputs[3])
         data = stack.get_data()
-        eq_(data.shape, stack.get_shape())
+        eq_(data.shape, stack.shape)
         eq_(sha256(data).hexdigest(),
             'bb3639a6ece13dc9a11d65f1b09ab3ccaed63b22dcf0f96fb5d3dd8805cc7b8a')
 
@@ -512,7 +512,7 @@ def test_allow_dummy(self):
         stack.add_dcm(self.inputs[0])
         stack.add_dcm(self.inputs[1])
         data = stack.get_data()
-        eq_(data.shape, stack.get_shape())
+        eq_(data.shape, stack.shape)
         ok_(np.all(data[:, :, -1] == np.iinfo(np.int16).max))
         eq_(sha256(data).hexdigest(),
             '7d85fbcb60a5021a45df3975613dcb7ac731830e0a268590cc798dc39897c04b')