RF: Remove deprecated nibabel image methods

Author: effigies

nipype/algorithms/confounds.py

@@ -398,7 +398,7 @@ def _run_interface(self, runtime):
         if len(mask_images) == 0:
             img = nb.Nifti1Image(np.ones(imgseries.shape[:3], dtype=np.bool),
                                  affine=imgseries.affine,
-                                 header=imgseries.get_header())
+                                 header=imgseries.header)
             mask_images = [img]
 
         mask_images = self._process_masks(mask_images, imgseries.get_data())
@@ -501,7 +501,7 @@ def _process_masks(self, mask_images, timeseries=None):
             mask_data = np.zeros_like(mask)
             mask_data[mask != 0] = tSTD >= threshold_std
             out_image = nb.Nifti1Image(mask_data, affine=img.affine,
-                                       header=img.get_header())
+                                       header=img.header)
 
             # save mask
             mask_file = os.path.abspath('mask_{:03d}.nii.gz'.format(i))
@@ -561,7 +561,7 @@ def _run_interface(self, runtime):
         header = img.header.copy()
         vollist = [nb.load(filename, mmap=NUMPY_MMAP) for filename in self.inputs.in_file]
         data = np.concatenate([vol.get_data().reshape(
-            vol.get_shape()[:3] + (-1,)) for vol in vollist], axis=3)
+            vol.shape[:3] + (-1,)) for vol in vollist], axis=3)
         data = np.nan_to_num(data)
 
         if data.dtype.kind == 'i':
@@ -570,18 +570,18 @@ def _run_interface(self, runtime):
 
         if isdefined(self.inputs.regress_poly):
             data = regress_poly(self.inputs.regress_poly, data, remove_mean=False)
-            img = nb.Nifti1Image(data, img.get_affine(), header)
+            img = nb.Nifti1Image(data, img.affine, header)
             nb.save(img, op.abspath(self.inputs.detrended_file))
 
         meanimg = np.mean(data, axis=3)
         stddevimg = np.std(data, axis=3)
         tsnr = np.zeros_like(meanimg)
         tsnr[stddevimg > 1.e-3] = meanimg[stddevimg > 1.e-3] / stddevimg[stddevimg > 1.e-3]
-        img = nb.Nifti1Image(tsnr, img.get_affine(), header)
+        img = nb.Nifti1Image(tsnr, img.affine, header)
         nb.save(img, op.abspath(self.inputs.tsnr_file))
-        img = nb.Nifti1Image(meanimg, img.get_affine(), header)
+        img = nb.Nifti1Image(meanimg, img.affine, header)
         nb.save(img, op.abspath(self.inputs.mean_file))
-        img = nb.Nifti1Image(stddevimg, img.get_affine(), header)
+        img = nb.Nifti1Image(stddevimg, img.affine, header)
         nb.save(img, op.abspath(self.inputs.stddev_file))
         return runtime
 
@@ -872,7 +872,7 @@ def combine_mask_files(mask_files, mask_method=None, mask_index=None):
             if mask is None:
                 mask = img.get_data() > 0
             np.logical_or(mask, img.get_data() > 0, mask)
-        img = nb.Nifti1Image(mask, img.affine, header=img.get_header())
+        img = nb.Nifti1Image(mask, img.affine, header=img.header)
         return [img]
 
     if mask_method == 'intersect':
@@ -882,7 +882,7 @@ def combine_mask_files(mask_files, mask_method=None, mask_index=None):
             if mask is None:
                 mask = img.get_data() > 0
             np.logical_and(mask, img.get_data() > 0, mask)
-        img = nb.Nifti1Image(mask, img.affine, header=img.get_header())
+        img = nb.Nifti1Image(mask, img.affine, header=img.header)
         return [img]
 
 

nipype/interfaces/dipy/reconstruction.py

@@ -74,8 +74,8 @@ def _run_interface(self, runtime):
         import gc
 
         img = nb.load(self.inputs.in_file)
-        hdr = img.get_header().copy()
-        affine = img.get_affine()
+        hdr = img.header.copy()
+        affine = img.affine
         data = img.get_data()
         gtab = self._get_gradient_table()
 
@@ -210,14 +210,14 @@ def _run_interface(self, runtime):
 
         img = nb.load(self.inputs.in_file)
         imref = nb.four_to_three(img)[0]
-        affine = img.get_affine()
+        affine = img.affine
 
         if isdefined(self.inputs.in_mask):
             msk = nb.load(self.inputs.in_mask).get_data()
             msk[msk > 0] = 1
             msk[msk < 0] = 0
         else:
-            msk = np.ones(imref.get_shape())
+            msk = np.ones(imref.shape)
 
         data = img.get_data().astype(np.float32)
         gtab = self._get_gradient_table()
@@ -326,15 +326,15 @@ def _run_interface(self, runtime):
 
         img = nb.load(self.inputs.in_file)
         imref = nb.four_to_three(img)[0]
-        affine = img.get_affine()
+        affine = img.affine
 
         if isdefined(self.inputs.in_mask):
             msk = nb.load(self.inputs.in_mask).get_data()
         else:
-            msk = np.ones(imref.get_shape())
+            msk = np.ones(imref.shape)
 
         data = img.get_data().astype(np.float32)
-        hdr = imref.get_header().copy()
+        hdr = imref.header.copy()
 
         gtab = self._get_gradient_table()
         resp_file = np.loadtxt(self.inputs.response)
@@ -359,7 +359,7 @@ def _run_interface(self, runtime):
         if self.inputs.save_fods:
             sphere = get_sphere('symmetric724')
             fods = csd_fit.odf(sphere)
-            nb.Nifti1Image(fods.astype(np.float32), img.get_affine(),
+            nb.Nifti1Image(fods.astype(np.float32), img.affine,
                            None).to_filename(self._gen_filename('fods'))
 
         return runtime

nipype/interfaces/dipy/tensors.py

@@ -127,7 +127,7 @@ def _run_interface(self, runtime):
         # Load the 4D image files
         img = nb.load(self.inputs.in_file)
         data = img.get_data()
-        affine = img.get_affine()
+        affine = img.affine
 
         # Load the gradient strengths and directions
         gtab = self._get_gradient_table()

nipype/interfaces/dipy/tracks.py

@@ -177,10 +177,10 @@ def _run_interface(self, runtime):
 
         img = nb.load(self.inputs.in_file)
         imref = nb.four_to_three(img)[0]
-        affine = img.get_affine()
+        affine = img.affine
 
         data = img.get_data().astype(np.float32)
-        hdr = imref.get_header().copy()
+        hdr = imref.header.copy()
         hdr.set_data_dtype(np.float32)
         hdr['data_type'] = 16
 
@@ -222,7 +222,7 @@ def _run_interface(self, runtime):
             msk[msk > 0] = 1
             msk[msk < 0] = 0
         else:
-            msk = np.ones(imref.get_shape())
+            msk = np.ones(imref.shape)
 
         gfa = peaks.gfa * msk
         seeds = self.inputs.num_seeds