def test_invalid_encoding(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Set the encoding to be incorrect
header['encoding'] = 'fake'
with self.assertRaisesRegex(nrrd.NRRDError, 'Unsupported encoding: "fake"'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_missing_required_field(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Delete required field
del header['type']
with self.assertRaisesRegex(nrrd.NRRDError, 'Header is missing required field: "type".'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_invalid_endian(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Set endianness to fake value
header['endian'] = 'fake'
with self.assertRaisesRegex(nrrd.NRRDError, 'Invalid endian value in header: "fake"'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_invalid_encoding(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Set the encoding to be incorrect
header['encoding'] = 'fake'
with self.assertRaisesRegex(nrrd.NRRDError,
'Unsupported encoding: "fake"'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_missing_endianness(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Delete the endian field from header
# Since our data is short (itemsize = 2), we should receive an error
del header['endian']
with self.assertRaisesRegex(nrrd.NRRDError, 'Header is missing required field: "endian".'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_invalid_lineskip(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Set the line skip to be incorrect
header['line skip'] = -1
with self.assertRaisesRegex(nrrd.NRRDError, 'Invalid lineskip, allowed values are greater than or equal to'
' 0'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_detached_header_no_filename(self):
self.expected_header[u'data file'] = os.path.basename(RAW_DATA_FILE_PATH)
with open(RAW_NHDR_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# No filename is specified for read_data
with self.assertRaisesRegex(nrrd.NRRDError, 'Filename parameter must be specified when a relative data file'
' path is given'):
nrrd.read_data(header, fh)
def test_wrong_sizes(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Make the number of dimensions wrong
header['dimension'] = 2
with self.assertRaisesRegex(nrrd.NRRDError, 'Number of elements in sizes does not match dimension. '
'Dimension: 2, len\\(sizes\\): 3'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_invalid_endian(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Set endianness to fake value
header['endian'] = 'fake'
with self.assertRaisesRegex(
nrrd.NRRDError, 'Invalid endian value in header: "fake"'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_missing_required_field(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Delete required field
del header['type']
with self.assertRaisesRegex(
nrrd.NRRDError,
'Header is missing required field: "type".'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_wrong_sizes(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Make the number of dimensions wrong
header['dimension'] = 2
with self.assertRaisesRegex(
nrrd.NRRDError,
'Number of elements in sizes does not match dimension. '
'Dimension: 2, len\\(sizes\\): 3'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_invalid_lineskip(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Set the line skip to be incorrect
header['line skip'] = -1
with self.assertRaisesRegex(
nrrd.NRRDError,
'Invalid lineskip, allowed values are greater than or equal to'
' 0'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_missing_endianness(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Delete the endian field from header
# Since our data is short (itemsize = 2), we should receive an error
del header['endian']
with self.assertRaisesRegex(
nrrd.NRRDError,
'Header is missing required field: "endian".'):
nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
def test_detached_header_no_filename(self):
self.expected_header[u'data file'] = os.path.basename(
RAW_DATA_FILE_PATH)
with open(RAW_NHDR_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# No filename is specified for read_data
with self.assertRaisesRegex(
nrrd.NRRDError,
'Filename parameter must be specified when a relative data file'
' path is given'):
nrrd.read_data(header, fh)
def read_nrrd(
self,
member: ZipMember) -> Tuple[np.ndarray, collections.OrderedDict]:
"""
Access, load and transform NRRD file member of the MRB file into
a numpy ndarray and corresponding header metadata.
Accessed member is specified via string or ZipInfo instance.
Parameters
----------
member : str or zipfile.ZipInfo
Internal path or ZipInfo instance pointing to the member.
Returns
-------
(data, header) : tuple
2-Tuple of the raw data and the NRRD file header.
The raw data is a numpy.ndarray.
"""
member_fobj = io.BytesIO(self.read(member))
header = nrrd.read_header(member_fobj)
data = nrrd.read_data(header, fh=member_fobj)
return (data, header)
def test_big_endian(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Set endianness to big to verify it is doing correctly
header['endian'] = 'big'
data = nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
np.testing.assert_equal(data, self.expected_data.byteswap())
def test_big_endian(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
np.testing.assert_equal(self.expected_header, header)
# Set endianness to big to verify it is doing correctly
header['endian'] = 'big'
data = nrrd.read_data(header, fh, RAW_NRRD_FILE_PATH)
np.testing.assert_equal(data, self.expected_data.byteswap())
def _read_mitk_field(archive, fieldpath):
""" mitk stores a zip archive with one nrrd file per label mask
read individual nrrd files into tempfiles, pass to internal nrrd io routines """
b = archive.read(fieldpath)
with tempfile.TemporaryFile() as tf:
tf.write(b)
tf.seek(0)
header = nrrd.read_header(tf)
data = nrrd.read_data(header, tf, None)
# data = np.transpose(data)
# mitk stores column-major 3D image....
# if data.ndim == 3:
# data = data[0]
return data
print res
with open(args.file, "rb") as inputnrrd:
header = nrrd.read_header(inputnrrd)
headerJson = json.dumps(header)
service = DVIDNodeService(addr, uid)
kvname = 'headers'
if service.create_keyvalue(kvname):
service.put(kvname, args.file, headerJson)
else:
service.put(kvname, args.file, headerJson)
# we should check if the key is there and warn the user to avoid overwriting when not desired
data = np.ascontiguousarray(nrrd.read_data(header, inputnrrd, args.file))
reshaper = []
for dim in data.shape:
if dim % 32 != 0:
newmax = (dim / 32 + 1) * 32
else:
newmax = dim
reshaper += [(0, newmax - dim)]
data = np.pad(data, reshaper, mode='constant')
d2 = data.copy()
data = None
pdb.set_trace()
import numpy as np
import nrrd
displacement = nrrd.read_data('Pt109 Displacement Field.nrrd')
print(displacement)
image = nrrd.read('Pt109_TransformedVolumes_1_12 frame1.nrrd')
print(image)
def load(filename):
log.info('Loading nrrd slice {}'.format(filename))
with open_file(filename) as fh:
header = nrrd.read_header(fh)
return nrrd.read_data(header, fh, filename), header
