def test_multipage_tiff(self):
from jicbioimage.core.image import MicroscopyCollection, ImageCollection
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(directory=TMP_DIR)
data_manager = DataManager(backend)
data_manager.load(os.path.join(DATA_DIR, 'multipage.tif'))
image_collection = data_manager[0]
# When we load a multipage tiff file we get an ImageCollection not a
# MicroscopyCollection.
self.assertFalse(isinstance(image_collection, MicroscopyCollection))
self.assertTrue(isinstance(image_collection, ImageCollection))
# Let us get the first proxy image.
first_proxy_image = image_collection.proxy_image()
self.assertTrue(os.path.isfile(first_proxy_image.fpath))
# Let us get the last proxy image.
last_proxy_image = image_collection.proxy_image(index=-1)
self.assertTrue(os.path.isfile(last_proxy_image.fpath))
# Let us get some actual images.
first_image = image_collection.image()
self.assertEqual(np.max(first_image), 30)
second_image = image_collection.image(1)
self.assertEqual(np.max(second_image), 90)
third_image = image_collection.image(index=2)
self.assertEqual(np.max(third_image), 120)
def test_manual_addition_of_ImageCollection_to_DataManager(self):
# We start off by creating a :class:`jicbioimage.core.io.DataManager`.
# This takes a backend argument. The backend provides a means to store
# unpacked image files.
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(directory=TMP_DIR)
data_manager = DataManager(backend=backend)
# The :func:`jicbioimage.core.image.DataManager.conver` function is be
# default an instance of the callable
# :class:`jicbioimage.core.io.BFConvertWrapper` class.
from jicbioimage.core.io import BFConvertWrapper, _md5_hexdigest_from_file
self.assertTrue(isinstance(data_manager.convert, BFConvertWrapper))
# We also need to import an ImageCollection
from jicbioimage.core.image import ImageCollection
# If the input file has not already been converted with do so.
fpath = os.path.join(DATA_DIR, 'z-series.ome.tif')
self.assertFalse(data_manager.convert.already_converted(fpath))
if not data_manager.convert.already_converted(fpath):
path_to_manifest = data_manager.convert(fpath) # unpacks and creates manifests
self.assertEqual(path_to_manifest, os.path.join(TMP_DIR,
_md5_hexdigest_from_file(fpath),
'manifest.json'))
image_collection = ImageCollection()
image_collection.parse_manifest(path_to_manifest)
self.assertEqual(len(image_collection), 5)
data_manager.append(image_collection)
self.assertEqual(len(data_manager), 1)
self.assertTrue(data_manager.convert.already_converted(fpath))
def test_error_message_when_bfconvert_not_in_path(self):
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(TMP_DIR)
data_manager = DataManager(backend)
tmp_path = os.environ['PATH']
del os.environ['PATH']
with self.assertRaises(RuntimeError):
data_manager.load(os.path.join(DATA_DIR, 'single-channel.ome.tif'))
os.environ['PATH'] = tmp_path
def test_load_returns_collection(self):
from jicbioimage.core.image import ImageCollection
from jicbioimage.core.image import MicroscopyImage, ProxyImage
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(directory=TMP_DIR)
data_manager = DataManager(backend)
collection = data_manager.load(os.path.join(DATA_DIR, 'multipage.tif'))
self.assertTrue(isinstance(collection, ImageCollection))
self.assertFalse(isinstance(collection[0], MicroscopyImage))
self.assertTrue(isinstance(collection[0], ProxyImage))
def get_microscopy_collection(input_file):
"""Return microscopy collection from input file."""
data_dir = os.path.abspath(os.path.join(HERE, "..", "data"))
if not os.path.isdir(data_dir):
os.mkdir(data_dir)
backend_dir = os.path.join(data_dir, 'unpacked')
file_backend = FileBackend(backend_dir)
data_manager = DataManager(file_backend)
microscopy_collection = data_manager.load(input_file)
return microscopy_collection
def test_proxy_image(self):
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(TMP_DIR)
data_manager = DataManager(backend)
data_manager.load(os.path.join(DATA_DIR, 'single-channel.ome.tif'))
microscopy_collection = data_manager[0]
proxy_image = microscopy_collection.proxy_image()
self.assertTrue(os.path.isfile(proxy_image.fpath),
'no such file: {}'.format(proxy_image.fpath))
self.assertTrue(isinstance(proxy_image.image, np.ndarray))
self.assertEqual(proxy_image.image.shape, (167, 439))
def test_BZ1(self):
"""
If the file backend creates a directory into which to unpack TIFFs, but
then fails for some reason (e.g. bfconvert is not in the path), it has
created a directory, but not a manifest. At this point, re-running the
unpack fails because the directory already exists, and:
os.mkdir(self.directory) throws an error.
"""
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(directory=TMP_DIR)
data_manager = DataManager(backend=backend)
fname = 'single-channel.ome.tif'
# The directory already exists.
os.mkdir(os.path.join(TMP_DIR, fname))
# The below throws if the bug is present.
data_manager.load(os.path.join(DATA_DIR, fname))
def test_image_collection(self):
from jicbioimage.core.image import Image3D
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(TMP_DIR)
data_manager = DataManager(backend)
data_manager.load(os.path.join(DATA_DIR, 'multi-channel-4D-series.ome.tif'))
microscopy_collection = data_manager[0]
self.assertEqual(len(microscopy_collection), 7*5*3) # 7t, 5z, 3c
proxy_image = microscopy_collection.proxy_image()
self.assertEqual(proxy_image.series, 0)
self.assertEqual(proxy_image.channel, 0)
self.assertEqual(proxy_image.zslice, 0)
self.assertEqual(proxy_image.timepoint, 0)
proxy_image = microscopy_collection.proxy_image(s=0, c=1, z=2, t=3)
self.assertEqual(proxy_image.series, 0)
self.assertEqual(proxy_image.channel, 1)
self.assertEqual(proxy_image.zslice, 2)
self.assertEqual(proxy_image.timepoint, 3)
self.assertEqual(5,
len([i for i in microscopy_collection.zstack_proxy_iterator()]))
for i, proxy_image in enumerate(microscopy_collection.zstack_proxy_iterator()):
self.assertEqual(proxy_image.series, 0)
self.assertEqual(proxy_image.channel, 0)
self.assertEqual(proxy_image.zslice, i)
self.assertEqual(proxy_image.timepoint, 0)
self.assertEqual(5,
len([i for i in microscopy_collection.zstack_proxy_iterator(s=0, c=1, t=3)]))
for i, proxy_image in enumerate(microscopy_collection.zstack_proxy_iterator(s=0, c=1, t=3)):
self.assertEqual(proxy_image.series, 0)
self.assertEqual(proxy_image.channel, 1)
self.assertEqual(proxy_image.zslice, i)
self.assertEqual(proxy_image.timepoint, 3)
zstack = microscopy_collection.zstack(s=0, c=1, t=3)
self.assertTrue(isinstance(zstack, Image3D))
self.assertEqual(zstack.shape, (167, 439, 5))
image = microscopy_collection.image(s=0, c=1, z=2, t=3)
self.assertTrue(isinstance(image, np.ndarray))
self.assertEqual(image.shape, (167, 439))
def test_stack_to_image_transform(self):
from jicbioimage.core.image import Image
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(TMP_DIR)
data_manager = DataManager(backend)
from jicbioimage.core.transform import transformation
from jicbioimage.core.io import AutoName
AutoName.directory = TMP_DIR
@transformation
def average_projection(stack):
xmax, ymax, zmax = stack.shape
projection = np.sum(stack, axis=2, dtype=np.uint8) // zmax
return Image.from_array(projection)
data_manager.load(os.path.join(DATA_DIR, 'z-series.ome.tif'))
microscopy_collection = data_manager[0]
stack = microscopy_collection.zstack()
image = average_projection(stack)
self.assertTrue(isinstance(image, Image))
def test_initialisation_without_explicit_backend(self):
from jicbioimage.core.io import DataManager
real_working_dir = os.getcwd()
try:
os.chdir(TMP_DIR)
data_manager = DataManager()
file_backend_path = os.path.join(os.getcwd(), 'jicbioimage.core_backend')
self.assertEqual(data_manager.backend.directory, file_backend_path)
finally:
os.chdir(real_working_dir)
def test_data_manager_already_unpacked(self):
# The second time the data manager is loaded, it should contain data
# without unpacking.
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(TMP_DIR)
data_manager = DataManager(backend)
data_manager.load(os.path.join(DATA_DIR, 'single-channel.ome.tif'))
self.assertEqual(len(data_manager), 1)
backend_reload = FileBackend(TMP_DIR)
data_manager_reload = DataManager(backend)
data_manager_reload.load(os.path.join(DATA_DIR, 'single-channel.ome.tif'))
self.assertEqual(len(data_manager_reload), 1)
def test_data_manager(self):
# Alice wants to analyse her microscopy data. To access the raw image
# data within the microscopy files she uses a DataManager.
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(TMP_DIR)
data_manager = DataManager(backend)
# Initially the DataManger is empty.
self.assertEqual(len(data_manager), 0)
# Alice loads her file of interest.
data_manager.load(os.path.join(DATA_DIR, 'single-channel.ome.tif'))
self.assertEqual(len(data_manager), 1)
# A DataManager is a container for MicroscopyCollection instances.
from jicbioimage.core.image import MicroscopyCollection
microscopy_collection = data_manager[0]
self.assertTrue(isinstance(microscopy_collection, MicroscopyCollection))
# In this instance the image collection only contains one item.
self.assertEqual(len(microscopy_collection), 1)
image = microscopy_collection[0]
# A MicroscopyCollection is a container for MicroscopyImage instances.
from jicbioimage.core.image import MicroscopyImage
self.assertTrue(isinstance(image, MicroscopyImage))
# Alice then loads her second file of interest.
data_manager.load(os.path.join(DATA_DIR, 'z-series.ome.tif'))
# The data manager now contains to image collections.
self.assertEqual(len(data_manager), 2)
# There are five z-slices in the new image collection.
zseries_collection = data_manager[1]
self.assertEqual(len(zseries_collection), 5)
# File format conversion trouble (for example using non existing input
# file) raises IOError.
with self.assertRaises(IOError):
data_manager.load(os.path.join(DATA_DIR, 'nonsese.ome.tif'))
def test_default_convert(self):
from jicbioimage.core.io import DataManager, BFConvertWrapper
data_manager = DataManager(os.path.join(TMP_DIR, 'dummy'))
self.assertTrue(isinstance(data_manager.convert, BFConvertWrapper))
def test_backend(self):
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(os.path.join(TMP_DIR, 'dummy'))
data_manager = DataManager(backend)
self.assertTrue(isinstance(data_manager.backend, FileBackend))
def test_load_function_exists(self):
from jicbioimage.core.io import DataManager
data_manager = DataManager(os.path.join(TMP_DIR, 'dummy'))
self.assertTrue(callable(data_manager.load))