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test_reading.py
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import io
import unittest
from typing import ClassVar
import numpy as np
from typing_extensions import Literal
import nrrd
from nrrd.tests.util import *
class Abstract:
class TestReadingFunctions(unittest.TestCase):
index_order: ClassVar[Literal['F', 'C']]
def setUp(self):
self.expected_header = {'dimension': 3,
'encoding': 'raw',
'endian': 'little',
'kinds': ['domain', 'domain', 'domain'],
'sizes': np.array([30, 30, 30]),
'space': 'left-posterior-superior',
'space directions': np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
'space origin': np.array([0, 0, 0]),
'type': 'short'}
self.expected_data = np.fromfile(RAW_DATA_FILE_PATH, np.int16).reshape((30, 30, 30))
if self.index_order == 'F':
self.expected_data = self.expected_data.T
def test_read_header_only(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
# np.testing.assert_equal is used to compare the headers because it will appropriately handle each
# value in the structure. Since some values can be Numpy arrays inside the headers, this must be used to
# compare the two values.
np.testing.assert_equal(self.expected_header, header)
def test_read_header_only_with_filename(self):
header = nrrd.read_header(RAW_NRRD_FILE_PATH)
# np.testing.assert_equal is used to compare the headers because it will appropriately handle each
# value in the structure. Since some values can be Numpy arrays inside the headers, this must be used to
# compare the two values.
np.testing.assert_equal(self.expected_header, header)
def test_read_detached_header_only(self):
expected_header = self.expected_header
expected_header['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)
def test_read_header_and_data_filename(self):
data, header = nrrd.read(RAW_NRRD_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(self.expected_header, header)
np.testing.assert_equal(data, self.expected_data)
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_detached_header_and_data(self):
expected_header = self.expected_header
expected_header['data file'] = os.path.basename(RAW_DATA_FILE_PATH)
data, header = nrrd.read(RAW_NHDR_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(self.expected_header, header)
np.testing.assert_equal(data, self.expected_data)
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_detached_header_and_data_with_byteskip_minus1(self):
expected_header = self.expected_header
expected_header['data file'] = os.path.basename(RAW_DATA_FILE_PATH)
expected_header['byte skip'] = -1
data, header = nrrd.read(RAW_BYTESKIP_NHDR_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(self.expected_header, header)
np.testing.assert_equal(data, self.expected_data)
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_detached_header_and_nifti_data_with_byteskip_minus1(self):
expected_header = self.expected_header
expected_header['data file'] = os.path.basename(RAW_DATA_FILE_PATH)
expected_header['byte skip'] = -1
expected_header['encoding'] = 'gzip'
expected_header['data file'] = 'BallBinary30x30x30.nii.gz'
data, header = nrrd.read(GZ_BYTESKIP_NIFTI_NHDR_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(self.expected_header, header)
np.testing.assert_equal(data, self.expected_data)
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_detached_header_and_nifti_data(self):
with self.assertRaisesRegex(
nrrd.NRRDError,
'Size of the data does not equal the product of all the dimensions: 27000-27176=-176'):
nrrd.read(GZ_NIFTI_NHDR_FILE_PATH, index_order=self.index_order)
def test_read_detached_header_and_data_with_byteskip_minus5(self):
with self.assertRaisesRegex(nrrd.NRRDError,
'Invalid byteskip, allowed values are greater than or equal to -1'):
nrrd.read(RAW_INVALID_BYTESKIP_NHDR_FILE_PATH, index_order=self.index_order)
def test_read_header_and_gz_compressed_data(self):
expected_header = self.expected_header
expected_header['encoding'] = 'gzip'
data, header = nrrd.read(GZ_NRRD_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(self.expected_header, header)
np.testing.assert_equal(data, self.expected_data)
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_header_and_gz_compressed_data_with_byteskip_minus1(self):
expected_header = self.expected_header
expected_header['encoding'] = 'gzip'
expected_header['type'] = 'int16'
expected_header['byte skip'] = -1
data, header = nrrd.read(GZ_BYTESKIP_NRRD_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(self.expected_header, header)
np.testing.assert_equal(data, self.expected_data)
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_header_and_bz2_compressed_data(self):
expected_header = self.expected_header
expected_header['encoding'] = 'bzip2'
data, header = nrrd.read(BZ2_NRRD_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(self.expected_header, header)
np.testing.assert_equal(data, self.expected_data)
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_header_and_gz_compressed_data_with_lineskip3(self):
expected_header = self.expected_header
expected_header['encoding'] = 'gzip'
expected_header['line skip'] = 3
data, header = nrrd.read(GZ_LINESKIP_NRRD_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(self.expected_header, header)
np.testing.assert_equal(data, self.expected_data)
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_raw_header(self):
expected_header = {'type': 'float', 'dimension': 3, 'min': 0, 'max': 35.4}
header = nrrd.read_header(('NRRD0005', 'type: float', 'dimension: 3', 'min: 0', 'max: 35.4'))
self.assertEqual(expected_header, header)
expected_header = {'my extra info': 'my : colon-separated : values'}
header = nrrd.read_header(('NRRD0005', 'my extra info:=my : colon-separated : values'))
np.testing.assert_equal(expected_header, header)
def test_read_dup_field_error_and_warn(self):
expected_header = {'type': 'float', 'dimension': 3}
header_txt_tuple = ('NRRD0005', 'type: float', 'dimension: 3', 'type: float')
with self.assertRaisesRegex(nrrd.NRRDError, 'Duplicate header field: type'):
header = nrrd.read_header(header_txt_tuple)
import warnings
with warnings.catch_warnings(record=True) as w:
nrrd.reader.ALLOW_DUPLICATE_FIELD = True
header = nrrd.read_header(header_txt_tuple)
self.assertTrue('Duplicate header field: type' in str(w[0].message))
self.assertEqual(expected_header, header)
nrrd.reader.ALLOW_DUPLICATE_FIELD = False
def test_read_header_and_ascii_1d_data(self):
expected_header = {'dimension': 1,
'encoding': 'ASCII',
'kinds': ['domain'],
'sizes': [27],
'spacings': [1.0458000000000001],
'type': 'unsigned char'}
data, header = nrrd.read(ASCII_1D_NRRD_FILE_PATH, index_order=self.index_order)
self.assertEqual(header, expected_header)
np.testing.assert_equal(data.dtype, np.uint8)
np.testing.assert_equal(data, np.arange(1, 28))
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_header_and_ascii_2d_data(self):
expected_header = {'dimension': 2,
'encoding': 'ASCII',
'kinds': ['domain', 'domain'],
'sizes': [3, 9],
'spacings': [1.0458000000000001, 2],
'type': 'unsigned short'}
data, header = nrrd.read(ASCII_2D_NRRD_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(header, expected_header)
np.testing.assert_equal(data.dtype, np.uint16)
expected_shape = (3, 9) if self.index_order == 'F' else (9, 3)
np.testing.assert_equal(data, np.arange(1, 28).reshape(expected_shape, order=self.index_order))
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_read_simple_4d_nrrd(self):
expected_header = {'type': 'double',
'dimension': 4,
'space': 'right-anterior-superior',
'sizes': np.array([1, 1, 1, 1]),
'space directions': np.array([[1.5, 0., 0.],
[0., 1.5, 0.],
[0., 0., 1.],
[np.nan, np.nan, np.nan]]),
'endian': 'little',
'encoding': 'raw',
'measurement frame': np.array([[1.0001, 0., 0.],
[0., 1.0000000006, 0.],
[0., 0., 1.000000000000009]])}
data, header = nrrd.read(RAW_4D_NRRD_FILE_PATH, index_order=self.index_order)
np.testing.assert_equal(header, expected_header)
np.testing.assert_equal(data.dtype, np.float64)
np.testing.assert_equal(header['measurement frame'].dtype, np.float64)
np.testing.assert_equal(data, np.array([[[[0.76903426]]]]))
# Test that the data read is able to be edited
self.assertTrue(data.flags['WRITEABLE'])
def test_custom_fields_without_field_map(self):
expected_header = {'dimension': 1,
'encoding': 'ASCII',
'kinds': ['domain'],
'sizes': [27],
'spacings': [1.0458000000000001],
'int': '24',
'double': '25.5566',
'string': 'This is a long string of information that is important.',
'int list': '1 2 3 4 5 100',
'double list': '0.2 0.502 0.8',
'string list': 'words are split by space in list',
'int vector': '(100, 200, -300)',
'double vector': '(100.5,200.3,-300.99)',
'int matrix': '(1,0,0) (0,1,0) (0,0,1)',
'double matrix': '(1.2,0.3,0) (0,1.5,0) (0,-0.55,1.6)',
'type': 'unsigned char'}
header = nrrd.read_header(ASCII_1D_CUSTOM_FIELDS_FILE_PATH)
self.assertEqual(header, expected_header)
def test_custom_fields_with_field_map(self):
expected_header = {'dimension': 1,
'encoding': 'ASCII',
'kinds': ['domain'],
'sizes': [27],
'spacings': [1.0458000000000001],
'int': 24,
'double': 25.5566,
'string': 'This is a long string of information that is important.',
'int list': np.array([1, 2, 3, 4, 5, 100]),
'double list': np.array([0.2, 0.502, 0.8]),
'string list': ['words', 'are', 'split', 'by', 'space', 'in', 'list'],
'int vector': np.array([100, 200, -300]),
'double vector': np.array([100.5, 200.3, -300.99]),
'int matrix': np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
'double matrix': np.array([[1.2, 0.3, 0.0], [0.0, 1.5, 0.0], [0.0, -0.55, 1.6]]),
'type': 'unsigned char'}
custom_field_map = {'int': 'int',
'double': 'double',
'string': 'string',
'int list': 'int list',
'double list': 'double list',
'string list': 'string list',
'int vector': 'int vector',
'double vector': 'double vector',
'int matrix': 'int matrix',
'double matrix': 'double matrix'}
header = nrrd.read_header(ASCII_1D_CUSTOM_FIELDS_FILE_PATH, custom_field_map)
np.testing.assert_equal(header, expected_header)
def test_invalid_custom_field(self):
custom_field_map = {'int': 'fake'}
with self.assertRaisesRegex(nrrd.NRRDError, 'Invalid field type given: fake'):
nrrd.read_header(ASCII_1D_CUSTOM_FIELDS_FILE_PATH, custom_field_map)
def test_invalid_magic_line(self):
with self.assertRaisesRegex(nrrd.NRRDError, 'Invalid NRRD magic line. Is this an NRRD file?'):
nrrd.read_header(('invalid magic line', 'my extra info:=my : colon-separated : values'))
def test_invalid_magic_line2(self):
with self.assertRaisesRegex(nrrd.NRRDError,
'Unsupported NRRD file version \\(version: 2000\\). This library '
'only supports v5 and below.'):
nrrd.read_header(('NRRD2000', 'my extra info:=my : colon-separated : values'))
def test_invalid_magic_line3(self):
with self.assertRaisesRegex(nrrd.NRRDError, 'Invalid NRRD magic line: NRRDnono'):
nrrd.read_header(('NRRDnono', 'my extra info:=my : colon-separated : values'))
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_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_detached_header_no_filename(self):
self.expected_header['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_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_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_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_index_order(self):
with self.assertRaisesRegex(nrrd.NRRDError, 'Invalid index order'):
nrrd.read(RAW_NRRD_FILE_PATH, index_order=None)
def test_read_quoted_string_header(self):
header = nrrd.read_header([
'NRRD0004',
'# Complete NRRD file format specification at:',
'# http://teem.sourceforge.net/nrrd/format.html',
'type: double',
'dimension: 3',
'space dimension: 3',
'sizes: 32 40 16',
'encoding: raw',
'units: "mm" "cm" "in"',
'space units: "mm" "cm" "in"',
'labels: "X" "Y" "f(log(X, 10), Y)"',
'space origin: (-0.79487200000000002,-1,-0.38461499999999998)'
])
# Check that the quoted values were appropriately parsed
self.assertEqual(['mm', 'cm', 'in'], header['units'])
self.assertEqual(['mm', 'cm', 'in'], header['space units'])
self.assertEqual(['X', 'Y', 'f(log(X, 10), Y)'], header['labels'])
def test_read_quoted_string_header_no_quotes(self):
header = nrrd.read_header([
'NRRD0004',
'# Complete NRRD file format specification at:',
'# http://teem.sourceforge.net/nrrd/format.html',
'type: double',
'dimension: 3',
'space dimension: 3',
'sizes: 32 40 16',
'encoding: raw',
'units: mm cm in',
'space units: mm cm in',
'labels: X Y f(log(X,10),Y)',
'space origin: (-0.79487200000000002,-1,-0.38461499999999998)'
])
# Check that the quoted values were appropriately parsed
self.assertEqual(['mm', 'cm', 'in'], header['units'])
self.assertEqual(['mm', 'cm', 'in'], header['space units'])
self.assertEqual(['X', 'Y', 'f(log(X,10),Y)'], header['labels'])
def test_read_memory(self):
def test(filename: str):
with open(filename, 'rb') as fh:
# Read into BytesIO and test that
x = fh.read()
memory_file = io.BytesIO(x)
memory_header = nrrd.read_header(memory_file)
memory_data = nrrd.read_data(memory_header, memory_file)
# Read normally via file handle
fh.seek(0)
expected_header = nrrd.read_header(fh)
expected_data = nrrd.read_data(expected_header, fh)
np.testing.assert_equal(expected_header, memory_header)
np.testing.assert_equal(expected_data, memory_data)
# Test that the data read is able to be edited
self.assertTrue(memory_data.flags['WRITEABLE'])
paths = [
RAW_NRRD_FILE_PATH,
GZ_NRRD_FILE_PATH,
GZ_BYTESKIP_NRRD_FILE_PATH,
GZ_LINESKIP_NRRD_FILE_PATH,
BZ2_NRRD_FILE_PATH,
ASCII_1D_NRRD_FILE_PATH,
ASCII_2D_NRRD_FILE_PATH,
RAW_4D_NRRD_FILE_PATH,
]
for filename in paths:
with self.subTest(filename):
test(filename)
def test_read_space_directions_list(self):
try:
nrrd.SPACE_DIRECTIONS_TYPE = 'double vector list'
_, header = nrrd.read(RAW_4D_NRRD_FILE_PATH, index_order=self.index_order)
self.assertIsInstance(header['space directions'], list)
self.assertTrue(
all(vector is None or isinstance(vector, np.ndarray) for vector in header['space directions']))
np.testing.assert_equal(header['space directions'][0].dtype, np.float64)
np.testing.assert_equal(header['space directions'], [np.array([1.5, 0., 0.]),
np.array([0., 1.5, 0.]),
np.array([0., 0., 1.]),
None])
finally:
nrrd.SPACE_DIRECTIONS_TYPE = 'double matrix'
def test_file_parameter_not_closed(self):
with open(RAW_NRRD_FILE_PATH, 'rb') as fh:
header = nrrd.read_header(fh)
nrrd.read_data(header, fh)
self.assertFalse(fh.closed)
class TestReadingFunctionsFortran(Abstract.TestReadingFunctions):
index_order = 'F'
class TestReadingFunctionsC(Abstract.TestReadingFunctions):
index_order = 'C'
if __name__ == '__main__':
unittest.main()