# Copyright 2011-2014 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import hashlib
import gzip
import os
from fastr.datatypes import URLType
[docs]class NiftiImageFileCompressed(URLType):
description = 'Compressed Nifti Image File format'
extension = 'nii.gz'
def _validate(self):
parsed_value = self.parsed_value
if self.extension and not parsed_value.endswith(self.extension):
return False
if not os.path.isfile(parsed_value):
return False
# Check magic bytes for Nifti-1 and Nifti-2 headers
# type depends on header size and the both have magic bits for
# identification
try:
with gzip.open(parsed_value, 'rb') as fin:
header_size_bytes = fin.read(4)
if len(header_size_bytes) != 4:
return False
header_size = int.from_bytes(header_size_bytes, 'little')
if header_size not in [348, 540]:
header_size = int.from_bytes(header_size_bytes, 'big')
if header_size == 348:
fin.seek(344)
magic = fin.read(4)
return magic == b'n+1\x00'
elif header_size == 540:
magic = fin.read(8)
return magic == b'\x6E\x2B\x32\x00\x0D\x0A\x1A\x0A'
else:
return False
except OSError:
# Not a valid gzip archive
return False
[docs] def checksum(self):
"""
Return the checksum of this URL type
:return: checksum string
:rtype: str
"""
contents = self.content(self.parsed_value)
hasher = hashlib.new('md5')
for path in contents:
with gzip.open(path, 'rb') as file_handle:
while True:
data = file_handle.read(32768)
if not data:
break
hasher.update(data)
return hasher.hexdigest()