update out_path

Author: josephmje

dmriprep/interfaces/images.py

@@ -1,12 +1,11 @@
 """Image tools interfaces."""
-import numpy as np
-import nibabel as nb
-from nipype.utils.filemanip import fname_presuffix
 from nipype import logging
 from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec, SimpleInterface, File
 )
 
+from dmriprep.utils.images import extract_b0, rescale_b0, median
+
 LOGGER = logging.getLogger('nipype.interface')
 
 
@@ -45,24 +44,6 @@ def _run_interface(self, runtime):
         return runtime
 
 
-def extract_b0(in_file, b0_ixs, newpath=None):
-    """Extract the *b0* volumes from a DWI dataset."""
-    out_file = fname_presuffix(
-        in_file, suffix='_b0', newpath=newpath)
-
-    img = nb.load(in_file)
-    data = img.get_fdata(dtype='float32')
-
-    b0 = data[..., b0_ixs]
-
-    hdr = img.header.copy()
-    hdr.set_data_shape(b0.shape)
-    hdr.set_xyzt_units('mm')
-    hdr.set_data_dtype(np.float32)
-    nb.Nifti1Image(b0, img.affine, hdr).to_filename(out_file)
-    return out_file
-
-
 class _RescaleB0InputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='b0s file')
     mask_file = File(exists=True, mandatory=True, desc='mask file')
@@ -101,45 +82,3 @@ def _run_interface(self, runtime):
             newpath=runtime.cwd
         )
         return runtime
-
-
-def rescale_b0(in_file, mask_file, newpath=None):
-    """Rescale the input volumes using the median signal intensity."""
-    out_file = fname_presuffix(
-        in_file, suffix='_rescaled_b0', newpath=newpath)
-
-    img = nb.load(in_file)
-    if img.dataobj.ndim == 3:
-        return in_file
-
-    data = img.get_fdata(dtype='float32')
-    mask_img = nb.load(mask_file)
-    mask_data = mask_img.get_fdata(dtype='float32')
-
-    median_signal = np.median(data[mask_data > 0, ...], axis=0)
-    rescaled_data = 1000 * data / median_signal
-    hdr = img.header.copy()
-    nb.Nifti1Image(rescaled_data, img.affine, hdr).to_filename(out_file)
-    return out_file
-
-
-def median(in_file, newpath=None):
-    """Average a 4D dataset across the last dimension using median."""
-    out_file = fname_presuffix(
-        in_file, suffix='_b0ref', newpath=newpath)
-
-    img = nb.load(in_file)
-    if img.dataobj.ndim == 3:
-        return in_file
-    if img.shape[-1] == 1:
-        nb.squeeze_image(img).to_filename(out_file)
-        return out_file
-
-    median_data = np.median(img.get_fdata(dtype='float32'),
-                            axis=-1)
-
-    hdr = img.header.copy()
-    hdr.set_xyzt_units('mm')
-    hdr.set_data_dtype(np.float32)
-    nb.Nifti1Image(median_data, img.affine, hdr).to_filename(out_file)
-    return out_file

dmriprep/utils/images.py

@@ -0,0 +1,66 @@
+import numpy as np
+import nibabel as nb
+from nipype.utils.filemanip import fname_presuffix
+
+
+def extract_b0(in_file, b0_ixs, out_path=None):
+    """Extract the *b0* volumes from a DWI dataset."""
+    if out_path is None:
+        out_path = fname_presuffix(
+            in_file, suffix='_b0', use_ext=True)
+
+    img = nb.load(in_file)
+    data = img.get_fdata(dtype='float32')
+
+    b0 = data[..., b0_ixs]
+
+    hdr = img.header.copy()
+    hdr.set_data_shape(b0.shape)
+    hdr.set_xyzt_units('mm')
+    hdr.set_data_dtype(np.float32)
+    nb.Nifti1Image(b0, img.affine, hdr).to_filename(out_path)
+    return out_path
+
+
+def rescale_b0(in_file, mask_file, out_path=None):
+    """Rescale the input volumes using the median signal intensity."""
+    if out_path is None:
+        out_path = fname_presuffix(
+            in_file, suffix='_rescaled_b0', use_ext=True)
+
+    img = nb.load(in_file)
+    if img.dataobj.ndim == 3:
+        return in_file
+
+    data = img.get_fdata(dtype='float32')
+    mask_img = nb.load(mask_file)
+    mask_data = mask_img.get_fdata(dtype='float32')
+
+    median_signal = np.median(data[mask_data > 0, ...], axis=0)
+    rescaled_data = 1000 * data / median_signal
+    hdr = img.header.copy()
+    nb.Nifti1Image(rescaled_data, img.affine, hdr).to_filename(out_path)
+    return out_path
+
+
+def median(in_file, out_path=None):
+    """Average a 4D dataset across the last dimension using median."""
+    if out_path is None:
+        out_path = fname_presuffix(
+            in_file, suffix='_b0ref', use_ext=True)
+
+    img = nb.load(in_file)
+    if img.dataobj.ndim == 3:
+        return in_file
+    if img.shape[-1] == 1:
+        nb.squeeze_image(img).to_filename(out_path)
+        return out_path
+
+    median_data = np.median(img.get_fdata(dtype='float32'),
+                            axis=-1)
+
+    hdr = img.header.copy()
+    hdr.set_xyzt_units('mm')
+    hdr.set_data_dtype(np.float32)
+    nb.Nifti1Image(median_data, img.affine, hdr).to_filename(out_path)
+    return out_path