def test_match_ext(self):
self.assertEqual(
libmag.match_ext("foo1/bar1/item1.ext1", "foo2/bar2/item2.ext2"),
"foo2/bar2/item2.ext1")
# if there is no extension in the path to match, it will retain its own extension
self.assertEqual(
libmag.match_ext("foo1/bar1/item1", "foo2/bar2/item2.ext2"),
"foo2/bar2/item2.ext2")
self.assertEqual(
libmag.match_ext("foo1/bar1/item1.ext1", "foo2/bar2/item2"),
"foo2/bar2/item2.ext1")
self.assertEqual(
libmag.match_ext("foo1/bar1/item1", "foo2/bar2/item2"),
"foo2/bar2/item2")
def load_registered_img(img_path,
reg_name,
get_sitk=False,
replace=None,
return_path=False):
"""Load atlas-based image that has been registered to another image.
Args:
img_path: Path as had been given to generate the registered images,
with the parent path of the registered images and base name of
the original image.
reg_name: Atlas image suffix to open.
get_sitk: True if the image should be returned as a SimpleITK image;
defaults to False, in which case the corresponding Numpy array will
be extracted instead.
replace: Numpy image with which to replace and overwrite the loaded
image. Defaults to None, in which case no replacement will take
place.
return_path (bool): True to return the path from which the image
was loaded; defaults to False.
Returns:
:obj:`np.ndarray`: The atlas-based image as a Numpy array, or a
:obj:`sitk.Image` object if ``get_sitk`` is True. Also returns the
loaded path if ``return_path`` is True.
Raises:
``FileNotFoundError`` if the path cannot be found.
"""
# prioritize registered image extension matched to that of main image
reg_img_path = reg_out_path(img_path, reg_name, True)
reg_img, reg_img_path = read_sitk(reg_img_path)
if reg_img is None:
# fallback to loading barren reg_name from img_path's dir
reg_img_path = os.path.join(os.path.dirname(img_path),
libmag.match_ext(img_path, reg_name))
reg_img, reg_img_path = read_sitk(reg_img_path)
if reg_img is None:
raise FileNotFoundError(
"could not find registered image from {} and {}".format(
img_path,
os.path.splitext(reg_name)[0]))
if replace is not None:
reg_img = replace_sitk_with_numpy(reg_img, replace)
sitk.WriteImage(reg_img, reg_img_path, False)
print("replaced {} with current registered image".format(reg_img_path))
if not get_sitk:
reg_img = sitk.GetArrayFromImage(reg_img)
return (reg_img, reg_img_path) if return_path else reg_img
def load_registered_img(
img_path: str,
reg_name: str,
get_sitk: bool = False,
return_path: bool = False
) -> Union[Union[np.ndarray, sitk.Image], Tuple[Union[np.ndarray, sitk.Image],
str]]:
"""Load atlas-based image that has been registered to another image.
Args:
img_path: Path as had been given to generate the registered
images, with the parent path of the registered images and base name
of the original image.
reg_name: Atlas image suffix to open. Can be an absolute path,
which will be used directly, ignoring ``img_path``.
get_sitk: True if the image should be returned as a SimpleITK
image; defaults to False, in which case the corresponding Numpy
array will be extracted instead.
return_path: True to return the path from which the image
was loaded; defaults to False.
Returns:
The atlas-based image as a Numpy array, or a :class:`sitk.Image`
object if ``get_sitk`` is True. Also returns the loaded path if
``return_path`` is True.
Raises:
``FileNotFoundError`` if the path cannot be found.
"""
reg_img_path = reg_name
if not os.path.isabs(reg_name):
# use suffix given as an absolute path directly; otherwise, get
# registered image extension matched to that of main image
reg_img_path = reg_out_path(img_path, reg_name, True)
reg_img, reg_img_path = read_sitk(reg_img_path)
if reg_img is None:
# fallback to loading barren reg_name from img_path's dir
reg_img_path = os.path.join(os.path.dirname(img_path),
libmag.match_ext(img_path, reg_name))
reg_img, reg_img_path = read_sitk(reg_img_path)
if reg_img is None:
raise FileNotFoundError(
"could not find registered image from {} and {}".format(
img_path,
os.path.splitext(reg_name)[0]))
if not get_sitk:
reg_img = sitk.GetArrayFromImage(reg_img)
return (reg_img, reg_img_path) if return_path else reg_img
def write_reg_images(imgs_write,
prefix,
copy_to_suffix=False,
ext=None,
prefix_is_dir=False):
"""Write registered images to file.
Args:
imgs_write: Dictionary of ``{suffix: image}``, where ``suffix``
is a registered images suffix, such as :const:``IMAGE_LABELS``,
and ``image`` is a SimpleITK image object. If the image does
not exist, the file will not be written.
prefix: Base path from which to construct registered file paths.
Parent directories will be created if necessary.
copy_to_suffix: If True, copy the output path to a file in the
same directory with ``suffix`` as the filename, which may
be useful when setting the registered images as the
main images in the directory. Defaults to False.
ext: Replace extension with this value if given; defaults to None.
prefix_is_dir (bool): True to treat ``prefix`` as a directory;
defaults to False to get the directory name of ``prefix``.
"""
# get parent directories and create them if necessary
target_dir = prefix if prefix_is_dir else os.path.dirname(prefix)
if len(target_dir) > 0 and not os.path.exists(target_dir):
os.makedirs(target_dir)
for suffix in imgs_write.keys():
# write a registered image file for each entry
img = imgs_write[suffix]
if img is None: continue
if ext: suffix = libmag.match_ext(ext, suffix)
out_path = reg_out_path(prefix, suffix)
sitk.WriteImage(img, out_path, False)
print("wrote registered image to", out_path)
if copy_to_suffix:
# copy metadata file to allow opening images from bare suffix name,
# such as when this atlas becomes the new atlas for registration
out_path_copy = os.path.join(target_dir, suffix)
shutil.copy(out_path, out_path_copy)
print("also copied to", out_path_copy)
def reg_out_path(file_path, reg_name, match_ext=False):
"""Generate a path for a file registered to another file.
Args:
file_path: Full path of file registered to. :attr:`config.series`
will be appended unless ``file_path`` is a directory.
reg_name: Suffix for type of registration, eg :const:``IMG_LABELS``.
match_ext: True to change the extension of ``reg_name`` to match
that of ``file_path``.
Returns:
str: Full path with the registered filename including appropriate
extension at the end.
"""
if match_ext:
reg_name = libmag.match_ext(file_path, reg_name)
if os.path.isdir(file_path):
return os.path.join(file_path, reg_name)
else:
file_path_base = importer.filename_to_base(file_path, config.series)
return file_path_base + "_" + reg_name