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155 lines
5.8 KiB
155 lines
5.8 KiB
import unittest
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from os import path
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import array
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import six
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import struct
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from nd2reader2.artificial import ArtificialND2
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from nd2reader2.common import get_version, parse_version, parse_date, _add_to_metadata, _parse_unsigned_char, \
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_parse_unsigned_int, _parse_unsigned_long, _parse_double, check_or_make_dir, _parse_string, _parse_char_array, \
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get_from_dict_if_exists, read_chunk
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from nd2reader2.exceptions import InvalidVersionError
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class TestCommon(unittest.TestCase):
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def setUp(self):
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dir_path = path.dirname(path.realpath(__file__))
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check_or_make_dir(path.join(dir_path, 'test_data/'))
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self.test_file = path.join(dir_path, 'test_data/test.nd2')
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def create_test_nd2(self):
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with ArtificialND2(self.test_file) as artificial:
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artificial.close()
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def test_parse_version_2(self):
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data = 'ND2 FILE SIGNATURE CHUNK NAME01!Ver2.2'
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actual = parse_version(data)
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expected = (2, 2)
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self.assertTupleEqual(actual, expected)
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def test_parse_version_3(self):
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data = 'ND2 FILE SIGNATURE CHUNK NAME01!Ver3.0'
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actual = parse_version(data)
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expected = (3, 0)
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self.assertTupleEqual(actual, expected)
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def test_parse_version_invalid(self):
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data = 'ND2 FILE SIGNATURE CHUNK NAME!Version2.2.3'
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self.assertRaises(InvalidVersionError, parse_version, data)
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def test_get_version_from_file(self):
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self.create_test_nd2()
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with open(self.test_file, 'rb') as fh:
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version_tuple = get_version(fh)
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self.assertTupleEqual(version_tuple, (3, 0))
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def test_parse_date_24(self):
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date_format = "%m/%d/%Y %H:%M:%S"
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date = '02/13/2016 23:43:37'
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textinfo = {six.b('TextInfoItem9'): six.b(date)}
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result = parse_date(textinfo)
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self.assertEqual(result.strftime(date_format), date)
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def test_parse_date_12(self):
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date_format = "%m/%d/%Y %I:%M:%S %p"
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date = '02/13/2016 11:43:37 PM'
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textinfo = {six.b('TextInfoItem9'): six.b(date)}
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result = parse_date(textinfo)
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self.assertEqual(result.strftime(date_format), date)
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def test_parse_date_exception(self):
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date = 'i am no date'
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textinfo = {six.b('TextInfoItem9'): six.b(date)}
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result = parse_date(textinfo)
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self.assertIsNone(result)
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def test_add_to_meta_simple(self):
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metadata = {}
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_add_to_metadata(metadata, 'test', 'value')
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self.assertDictEqual(metadata, {'test': 'value'})
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def test_add_to_meta_new_list(self):
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metadata = {'test': 'value1'}
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_add_to_metadata(metadata, 'test', 'value2')
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self.assertDictEqual(metadata, {'test': ['value1', 'value2']})
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def test_add_to_meta_existing_list(self):
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metadata = {'test': ['value1', 'value2']}
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_add_to_metadata(metadata, 'test', 'value3')
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self.assertDictEqual(metadata, {'test': ['value1', 'value2', 'value3']})
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@staticmethod
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def _prepare_bin_stream(binary_format, *value):
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file = six.BytesIO()
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data = struct.pack(binary_format, *value)
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file.write(data)
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file.seek(0)
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return file
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def test_parse_functions(self):
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file = self._prepare_bin_stream("B", 9)
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self.assertEqual(_parse_unsigned_char(file), 9)
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file = self._prepare_bin_stream("I", 333)
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self.assertEqual(_parse_unsigned_int(file), 333)
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file = self._prepare_bin_stream("Q", 7564332)
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self.assertEqual(_parse_unsigned_long(file), 7564332)
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file = self._prepare_bin_stream("d", 47.9)
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self.assertEqual(_parse_double(file), 47.9)
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test_string = 'colloid'
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file = self._prepare_bin_stream("%ds" % len(test_string), six.b(test_string))
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parsed = _parse_string(file)
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self.assertEqual(parsed, six.b(test_string))
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test_data = [1, 2, 3, 4, 5]
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file = self._prepare_bin_stream("Q" + ''.join(['B'] * len(test_data)), len(test_data), *test_data)
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parsed = _parse_char_array(file)
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self.assertEqual(parsed, array.array('B', test_data))
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def test_get_from_dict_if_exists(self):
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test_dict = {
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six.b('existing'): 'test',
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'string': 'test2'
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}
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self.assertIsNone(get_from_dict_if_exists('nowhere', test_dict))
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self.assertEqual(get_from_dict_if_exists('existing', test_dict), 'test')
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self.assertEqual(get_from_dict_if_exists('string', test_dict, convert_key_to_binary=False), 'test2')
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def test_read_chunk(self):
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with ArtificialND2(self.test_file) as artificial:
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fh = artificial.file_handle
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chunk_location = artificial.locations['image_attributes'][0]
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chunk_read = read_chunk(fh, chunk_location)
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real_data = six.BytesIO(artificial.raw_text)
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real_data.seek(chunk_location)
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# The chunk metadata is always 16 bytes long
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chunk_metadata = real_data.read(16)
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header, relative_offset, data_length = struct.unpack("IIQ", chunk_metadata)
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self.assertEquals(header, 0xabeceda)
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# We start at the location of the chunk metadata, skip over the metadata, and then proceed to the
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# start of the actual data field, which is at some arbitrary place after the metadata.
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real_data.seek(chunk_location + 16 + relative_offset)
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real_chunk = real_data.read(data_length)
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self.assertEqual(real_chunk, chunk_read)
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def test_read_chunk_fail_bad_header(self):
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with ArtificialND2(self.test_file) as artificial:
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fh = artificial.file_handle
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chunk_location = artificial.locations['image_attributes'][0]
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with self.assertRaises(ValueError) as context:
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read_chunk(fh, chunk_location + 1)
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self.assertEquals(str(context.exception), "The ND2 file seems to be corrupted.")
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