def validate_and_fix_input_data(self, path: Path) -> Tuple[Path, bool]:
"""
Validate the provided data path and creates an unzipped version if
required.
Parameters
----------
path : Path
Path to input data
Returns
-------
Tuple[Path, bool]
Fixed input data path, whether is was unzipped or not
"""
path = self.nifti_validator.validate_and_fix(path)
# If the input is zipped, check for an existing unzipped version or
# create one.
if path.suffix == ".gz":
# In case un unzipped version exists already, return the unzipped
# version and 'False' for having created it.
if path.with_suffix("").is_file():
return path.with_suffix(""), False
# Otherwise, create an unzipped version and return 'True' for
# having created it.
return uncompress(path), True
return path, False
def validate_and_fix_input_data(self, scans: List[Path]) -> List[Path]:
"""
Validate the provided data path and creates an unzipped version if
required.
Parameters
----------
path : List[Path]
List of T1-weighted scan paths
Returns
-------
List[tuple]
List of tuples with shape (path string, created)
"""
scans = [self.nifti_validator.validate_and_fix(path) for path in scans]
results = []
for path in scans:
# If the input is zipped, check for an existing unzipped version or
# create one.
if path.suffix == ".gz":
# In case un unzipped version exists already, return the
# unzipped version and 'False' for having created it.
if path.with_suffix("").is_file():
results.append((path.with_suffix(""), False))
# Otherwise, create an unzipped version and return 'True' for
# having created it.
results.append(uncompress(path), True)
else:
results.append((path, False))
return results
def uncompress(self, keep_source: bool = False) -> Path:
if self.is_compressed:
compressed_path = Path(self.path)
uncompressed_path = uncompress(compressed_path,
keep_source=keep_source)
self.path = str(uncompressed_path)
self.save()
return Path(self.path)
def validate_and_fix_input_data(self, path: Path) -> tuple:
# Validate configuration
self.check_resampling_type()
path = self.nifti_validator.validate_and_fix(path)
# If the input is zipped, check for an existing unzipped version or create one
if path.suffix == ".gz":
# In case un unzipped version exists already, return the unzipped version
# and 'False' for having created it
if path.with_suffix("").is_file():
return path.with_suffix(""), False
# Otherwise, create an unzipped version and return 'True' for having created it
return uncompress(path), True
return path, False
def uncompress(self, keep_source: bool = False) -> Path:
"""
Uncompress the associated *.nii* using gzip, if it isn't already
uncompressed.
Parameters
----------
keep_source : bool, optional
Whether to keep a copy of the compressed file, by default False
Returns
-------
Path
Path of the uncompressed (*.nii*) file
"""
if self.is_compressed:
compressed_path = Path(self.path)
uncompressed_path = uncompress(compressed_path,
keep_source=keep_source)
self.path = str(uncompressed_path)
self.save()
return Path(self.path)