def test_get_num_positions_mm2gamma(setup_test_data,
setup_mm2gamma_singlepage_tiffs):
fold = setup_test_data
_, _, rand_folder = setup_mm2gamma_singlepage_tiffs
mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)
assert (mmr.get_num_positions() >= 1)
def test_get_array_mm2gamma(setup_test_data, setup_mm2gamma_singlepage_tiffs):
fold = setup_test_data
_, _, rand_folder = setup_mm2gamma_singlepage_tiffs
mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)
for i in range(mmr.get_num_positions()):
z = mmr.get_array(i)
assert (z.shape == mmr.shape)
assert (isinstance(z, np.ndarray))
def test_get_zarr_mm1422(setup_test_data, setup_mm1422_singlepage_tiffs):
fold = setup_test_data
_, _, rand_folder = setup_mm1422_singlepage_tiffs
mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)
for i in range(mmr.get_num_positions()):
z = mmr.get_zarr(i)
assert (z.shape == mmr.shape)
assert (isinstance(z, zarr.core.Array))
def test_output_dims_mm1422(setup_test_data, setup_mm1422_singlepage_tiffs):
"""
test that output dimensions are always (t, c, z, y, x)
"""
# choose a random folder
fold = setup_test_data
_, _, rand_folder = setup_mm1422_singlepage_tiffs
mmr = MicromanagerSequenceReader(rand_folder, extract_data=False)
assert (mmr.get_zarr(0).shape[0] == mmr.frames)
assert (mmr.get_zarr(0).shape[1] == mmr.channels)
assert (mmr.get_zarr(0).shape[2] == mmr.slices)
assert (mmr.get_zarr(0).shape[3] == mmr.height)
assert (mmr.get_zarr(0).shape[4] == mmr.width)
def test_output_dims_mm2gamma_incomplete(
setup_test_data, setup_mm2gamma_singlepage_tiffs_incomplete):
"""
test that output dimensions are correct for interrupted data
"""
# choose a random folder
fold = setup_test_data
folder = setup_mm2gamma_singlepage_tiffs_incomplete
mmr = MicromanagerSequenceReader(folder, extract_data=True)
assert (mmr.get_zarr(0).shape[0] == mmr.frames)
assert (mmr.get_zarr(0).shape[1] == mmr.channels)
assert (mmr.get_zarr(0).shape[2] == mmr.slices)
assert (mmr.get_zarr(0).shape[3] == mmr.height)
assert (mmr.get_zarr(0).shape[4] == mmr.width)
assert (mmr.get_zarr(0).shape[0] == 11)
def test_constructor_mm1422(setup_test_data, setup_mm1422_singlepage_tiffs):
"""
test that constructor parses metadata properly
no data extraction in this test
"""
# choose a specific folder
fold = setup_test_data
_, one_folder, _ = setup_mm1422_singlepage_tiffs
mmr = MicromanagerSequenceReader(one_folder, extract_data=False)
assert (mmr.mm_meta is not None)
assert (mmr.width is not 0)
assert (mmr.height is not 0)
assert (mmr.frames is not 0)
assert (mmr.slices is not 0)
assert (mmr.channels is not 0)
def __init__(self,
src: str,
data_type: str = None,
extract_data: bool = False,
log_level: int = logging.ERROR):
"""
reads data output from micro-manager and returns a zarr array or numpy array
supports singlepage tiff sequences or ome-tiffs
Parameters
----------
src: (str) folder or file containing all ome-tiff files or zarr root
data_type: (str) whether data is 'ometiff', 'singlepagetiff', or 'zarr'
extract_data: (bool) True if ome_series should be extracted immediately
log_level: (int) One of 0, 10, 20, 30, 40, 50 for NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL respectively
"""
logging.basicConfig(
level=log_level,
format=
"[%(levelname)4s: %(module)s:%(lineno)4s %(asctime)s] %(message)s",
)
self.log = logging.getLogger(__name__)
# catch if the user accidentally specifies one of the tiff files and not the parent folder
if data_type == 'ometiff':
if src.endswith('.tif'):
src = os.path.dirname(src)
if len(glob.glob(os.path.join(src, '*.tif'))) == 0:
raise FileNotFoundError(
'Specified folder does not contain any ome.tif files')
# Try to infer datatype
if not data_type:
try:
zarr.open(src, 'r')
data_type = 'zarr'
except:
if os.path.exists(src):
if src.endswith('.tif'):
src = os.path.dirname(src)
files = glob.glob(os.path.join(src, '*.tif'))
if len(files) == 0:
sub_dirs = self._get_sub_dirs(src)
if sub_dirs:
path = os.path.join(src, sub_dirs[0])
files = glob.glob(os.path.join(path, '*.tif'))
if len(files) == 0:
raise FileNotFoundError(
f'No compatible data found under {src}')
else:
with tiff.TiffFile(os.path.join(
path, files[0])) as tf:
if len(tf.pages) == 1 and tf.pages[
0].is_multipage.name == 'UNDEFINED':
data_type = 'singlepagetiff'
else:
raise FileNotFoundError(
f'No compatible data found under {src}, please specify the top '
'level micromanager directory')
else:
with tiff.TiffFile(files[0]) as tf:
if len(tf.pages) > 1:
data_type = 'ometiff'
else:
if tf.pages[
0].is_multipage == 0 and tf.is_ome == True:
data_type = 'ometiff'
else:
raise FileNotFoundError(
f'No compatible data found under {src}'
)
else:
raise FileExistsError(f'{src} does not exist')
# identify data structure type
if data_type == 'ometiff':
self.reader = MicromanagerOmeTiffReader(src, extract_data)
elif data_type == 'singlepagetiff':
self.reader = MicromanagerSequenceReader(src, extract_data)
elif data_type == 'zarr':
self.reader = ZarrReader(src)
elif data_type == 'upti':
self.reader = UPTIReader(src, extract_data)
else:
raise NotImplementedError(
f"reader of type {data_type} is not implemented")