def test_init_empty_file(self):
with ArtificialND2('test_data/empty.nd2',
skip_blocks=['label_map_marker']):
with self.assertRaises(EmptyFileError) as exception:
with ND2Reader('test_data/empty.nd2'):
pass
self.assertEqual(str(exception.exception),
"No axes were found for this .nd2 file.")
def test_read_chunk_fail_bad_header(self):
with ArtificialND2(self.test_file) as artificial:
fh = artificial.file_handle
chunk_location = artificial.locations['image_attributes'][0]
with self.assertRaises(ValueError) as context:
read_chunk(fh, chunk_location + 1)
self.assertEquals(str(context.exception), "The ND2 file seems to be corrupted.")
def test_get_frame_2D(self):
# Best test we can do for now:
# test everything up to the actual unpacking of the frame data
with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
with self.assertRaises(struct.error) as exception:
frame = reader.get_frame_2D(c=0, t=0, z=0, x=0, y=0, v=0)
self.assertIn('unpack', str(exception.exception))
def test_init_and_init_axes(self):
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
attributes = artificial.data['image_attributes']['SLxImageAttributes']
self.assertEqual(reader.metadata['width'], attributes['uiWidth'])
self.assertEqual(reader.metadata['height'], attributes['uiHeight'])
self.assertEqual(reader.metadata['width'], reader.sizes['x'])
self.assertEqual(reader.metadata['height'], reader.sizes['y'])
self.assertEqual(reader.pixel_type, np.float64)
self.assertEqual(reader.iter_axes, ['t'])
def test_init(self):
with ArtificialND2('test_data/legacy.nd2'):
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
with Nd2('test_data/legacy.nd2') as reader:
self.assertIsInstance(reader.reader, ND2Reader)
self.assertTrue(issubclass(w[0].category, DeprecationWarning))
self.assertEquals(
str(w[0].message),
"The 'Nd2' class is deprecated, please consider using the new"
+ " ND2Reader interface which uses pims.")
def test_misc(self):
with ArtificialND2('test_data/legacy.nd2'):
with Nd2('test_data/legacy.nd2') as reader:
representation = "\n".join([
"<Deprecated ND2 %s>" % reader.reader.filename,
"Created: Unknown",
"Image size: %sx%s (HxW)" % (reader.height, reader.width),
"Frames: %s" % len(reader.frames),
"Channels: %s" % ", ".join(
["%s" % str(channel) for channel in reader.channels]),
"Fields of View: %s" % len(reader.fields_of_view),
"Z-Levels: %s" % len(reader.z_levels)
])
self.assertEquals(representation, str(reader))
# not implemented yet
self.assertEquals(reader.pixel_microns, None)
self.assertEquals(len(reader), 1)
def test_read_chunk(self):
with ArtificialND2(self.test_file) as artificial:
fh = artificial.file_handle
chunk_location = artificial.locations['image_attributes'][0]
chunk_read = read_chunk(fh, chunk_location)
real_data = six.BytesIO(artificial.raw_text)
real_data.seek(chunk_location)
# The chunk metadata is always 16 bytes long
chunk_metadata = real_data.read(16)
header, relative_offset, data_length = struct.unpack("IIQ", chunk_metadata)
self.assertEquals(header, 0xabeceda)
# We start at the location of the chunk metadata, skip over the metadata, and then proceed to the
# start of the actual data field, which is at some arbitrary place after the metadata.
real_data.seek(chunk_location + 16 + relative_offset)
real_chunk = real_data.read(data_length)
self.assertEqual(real_chunk, chunk_read)
def setUp(self):
self.nd2 = ArtificialND2('test_data/test_nd2_raw_metadata001.nd2')
self.raw_text, self.locations, self.file_data = self.nd2.raw_text, self.nd2.locations, self.nd2.data
self.label_map = LabelMap(self.raw_text)
self.metadata = RawMetadata(self.nd2.file_handle, self.label_map)
def create_test_nd2(self):
with ArtificialND2(self.test_file) as artificial:
self.assertIsNotNone(artificial.file_handle)
artificial.close()
def test_get_timesteps(self):
with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
timesteps = reader.timesteps
self.assertEquals(len(timesteps), 0)
def test_get_parser(self):
with ArtificialND2('test_data/test_nd2_reader.nd2') as _:
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
self.assertIsInstance(reader.parser, Parser)
def test_init_from_handler(self):
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
with open('test_data/test_nd2_reader.nd2', "rb") as FH:
with ND2Reader(FH) as reader:
self.cmp_two_readers(artificial, reader)
def test_init_and_init_axes(self):
with ArtificialND2('test_data/test_nd2_reader.nd2') as artificial:
with ND2Reader('test_data/test_nd2_reader.nd2') as reader:
self.cmp_two_readers(artificial, reader)
def create_test_nd2(self):
with ArtificialND2(self.test_file) as artificial:
artificial.close()
def setUp(self):
self.nd2 = ArtificialND2('test_data/test_nd2_label_map001.nd2')
self.raw_text, self.locations = self.nd2.raw_text, self.nd2.locations
self.label_map = LabelMap(self.raw_text)