def test_load_imgs_from_tree():
# test loading from within fov directories
with tempfile.TemporaryDirectory() as temp_dir:
fovs, chans, imgs = test_utils.gen_fov_chan_names(num_fovs=3, num_chans=3,
return_imgs=True)
filelocs, data_xr = test_utils.create_paired_xarray_fovs(
temp_dir, fovs, chans, img_shape=(10, 10), delimiter='_', fills=True, sub_dir="TIFs",
dtype="int16"
)
# check default loading of all files
loaded_xr = \
load_utils.load_imgs_from_tree(temp_dir, img_sub_folder="TIFs", dtype="int16")
assert loaded_xr.equals(data_xr)
# check loading of specific files
some_fovs = fovs[:2]
some_imgs = imgs[:2]
some_chans = chans[:2]
loaded_xr = \
load_utils.load_imgs_from_tree(temp_dir, img_sub_folder="TIFs", dtype="int16",
fovs=some_fovs, channels=some_imgs)
assert loaded_xr.equals(data_xr[:2, :, :, :2])
# check loading w/o file extension
loaded_xr = \
load_utils.load_imgs_from_tree(temp_dir, img_sub_folder="TIFs", dtype="int16",
channels=some_chans)
assert loaded_xr.equals(data_xr[:, :, :, :2], )
# check mixed extension presence
loaded_xr = \
load_utils.load_imgs_from_tree(temp_dir, img_sub_folder="TIFs", dtype="int16",
channels=[chans[i] if i % 2 else imgs[i]
for i in range(3)])
assert loaded_xr.equals(data_xr)
with tempfile.TemporaryDirectory() as temp_dir:
fovs, chans, imgs = test_utils.gen_fov_chan_names(num_fovs=1, num_chans=2,
return_imgs=True)
filelocs, data_xr = test_utils.create_paired_xarray_fovs(
temp_dir, fovs, chans, img_shape=(10, 10), delimiter='_', fills=True, sub_dir="TIFs",
dtype=np.float32
)
with pytest.warns(UserWarning):
loaded_xr = \
load_utils.load_imgs_from_tree(temp_dir, img_sub_folder="TIFs", dtype="int16")
assert loaded_xr.equals(data_xr)
# test swap int16 -> float
assert np.issubdtype(loaded_xr.dtype, np.floating)
def test_generate_cell_data_mibitiff_loading():
# is_mibitiff True case, load from mibitiff file structure
with tempfile.TemporaryDirectory() as temp_dir:
# define 3 fovs and 2 mibitiff_imgs
fovs, channels = test_utils.gen_fov_chan_names(3, 2)
# define a subset of fovs
fovs_subset = fovs[:2]
tiff_dir = os.path.join(temp_dir, "mibitiff_inputs")
os.mkdir(tiff_dir)
test_utils.create_paired_xarray_fovs(base_dir=tiff_dir,
fov_names=fovs,
channel_names=channels,
img_shape=(40, 40),
mode='mibitiff',
dtype=np.float32)
# generate a sample segmentation_mask
cell_mask, _ = test_utils.create_test_extraction_data()
cell_masks = np.zeros((3, 40, 40, 1), dtype="int16")
cell_masks[0, :, :, 0] = cell_mask[0, :, :, 0]
cell_masks[1, 5:, 5:, 0] = cell_mask[0, :-5, :-5, 0]
cell_masks[2, 10:, 10:, 0] = cell_mask[0, :-10, :-10, 0]
segmentation_masks = test_utils.make_labels_xarray(
label_data=cell_masks, compartment_names=['whole_cell'])
# generate sample norm and arcsinh data for all fovs
norm_data, arcsinh_data = marker_quantification.generate_cell_data(
segmentation_labels=segmentation_masks,
tiff_dir=tiff_dir,
img_sub_folder=tiff_dir,
is_mibitiff=True,
fovs=None,
batch_size=2)
assert norm_data.shape[0] > 0 and norm_data.shape[1] > 0
assert arcsinh_data.shape[0] > 0 and arcsinh_data.shape[1] > 0
# generate sample norm and arcsinh data for a subset of fovs
norm_data, arcsinh_data = marker_quantification.generate_cell_data(
segmentation_labels=segmentation_masks,
tiff_dir=tiff_dir,
img_sub_folder=tiff_dir,
is_mibitiff=True,
fovs=fovs_subset,
batch_size=2)
assert norm_data.shape[0] > 0 and norm_data.shape[1] > 0
assert arcsinh_data.shape[0] > 0 and arcsinh_data.shape[1] > 0
def test_split_img_stack():
with tempfile.TemporaryDirectory() as temp_dir:
fovs = ['stack_sample']
_, chans, names = test_utils.gen_fov_chan_names(num_fovs=0, num_chans=10, return_imgs=True)
stack_list = ["stack_sample.tiff"]
stack_dir = os.path.join(temp_dir, fovs[0])
os.mkdir(stack_dir)
output_dir = os.path.join(temp_dir, "output_sample")
os.mkdir(output_dir)
filelocs, data_xr = test_utils.create_paired_xarray_fovs(stack_dir, fovs,
chans, img_shape=(128, 128),
mode='multitiff')
# first test channel_first=False
data_utils.split_img_stack(stack_dir, output_dir, stack_list, [0, 1], names[0:2],
channels_first=False)
assert os.path.exists(os.path.join(output_dir, "stack_sample", "chan0.tiff"))
assert os.path.exists(os.path.join(output_dir, "stack_sample", "chan1.tiff"))
sample_chan_1 = io.imread(os.path.join(output_dir, "stack_sample", "chan0.tiff"))
sample_chan_2 = io.imread(os.path.join(output_dir, "stack_sample", "chan1.tiff"))
assert np.array_equal(sample_chan_1, data_xr[0, :, :, 0].values)
assert np.array_equal(sample_chan_2, data_xr[0, :, :, 1].values)
rmtree(os.path.join(output_dir, 'stack_sample'))
# now overwrite old stack_sample.jpg file and test channel_first=True
filelocs, data_xr = test_utils.create_paired_xarray_fovs(stack_dir, fovs,
chans, img_shape=(128, 128),
mode='reverse_multitiff')
data_utils.split_img_stack(stack_dir, output_dir, stack_list, [0, 1], names[0:2],
channels_first=True)
assert os.path.exists(os.path.join(output_dir, "stack_sample", "chan0.tiff"))
assert os.path.exists(os.path.join(output_dir, "stack_sample", "chan1.tiff"))
sample_chan_1 = io.imread(os.path.join(output_dir, "stack_sample", "chan0.tiff"))
sample_chan_2 = io.imread(os.path.join(output_dir, "stack_sample", "chan1.tiff"))
assert np.array_equal(sample_chan_1, data_xr[0, :, :, 0].values)
assert np.array_equal(sample_chan_2, data_xr[0, :, :, 1].values)
def test_load_imgs_from_mibitiff():
with tempfile.TemporaryDirectory() as temp_dir:
# config test environment
fovs, channels = test_utils.gen_fov_chan_names(num_fovs=2, num_chans=3, use_delimiter=True)
filelocs, data_xr = test_utils.create_paired_xarray_fovs(
temp_dir, fovs, channels, img_shape=(10, 10), mode='mibitiff', delimiter='_',
fills=True, dtype=np.float32
)
# check unspecified fov loading
loaded_xr = load_utils.load_imgs_from_mibitiff(temp_dir,
channels=channels,
delimiter='_')
assert loaded_xr.equals(data_xr)
fovnames = [f'{fov}.tiff' for fov in fovs]
# check specified fov loading
loaded_xr = load_utils.load_imgs_from_mibitiff(temp_dir,
mibitiff_files=[fovnames[-1]],
channels=channels,
delimiter='_')
assert loaded_xr.equals(data_xr.loc[[fovs[-1]], :, :, :])
# test automatic all channels loading
loaded_xr = load_utils.load_imgs_from_mibitiff(temp_dir,
delimiter='_',
dtype=np.float32)
assert loaded_xr.equals(data_xr)
# test delimiter agnosticism
loaded_xr = load_utils.load_imgs_from_mibitiff(temp_dir,
mibitiff_files=fovnames,
channels=channels,
delimiter='_',
dtype=np.float32)
assert loaded_xr.equals(data_xr)
assert np.issubdtype(loaded_xr.dtype, np.floating)
# test float overwrite
with pytest.warns(UserWarning):
loaded_xr = load_utils.load_imgs_from_mibitiff(temp_dir,
mibitiff_files=[fovnames[-1]],
channels=channels,
delimiter='_',
dtype='int16')
assert loaded_xr.equals(data_xr.loc[[fovs[-1]], :, :, :])
assert np.issubdtype(loaded_xr.dtype, np.floating)
def test_load_imgs_from_dir():
# test loading from 'free' directory
with tempfile.TemporaryDirectory() as temp_dir:
fovs, _ = test_utils.gen_fov_chan_names(num_fovs=3, num_chans=0, use_delimiter=True)
filelocs, data_xr = test_utils.create_paired_xarray_fovs(temp_dir, fovs, ['img_data'],
img_shape=(10, 10), mode='labels',
delimiter='_', dtype=np.float32)
# check default loading
loaded_xr = \
load_utils.load_imgs_from_dir(temp_dir, delimiter='_', dtype=np.float32)
assert loaded_xr.equals(data_xr)
# test swap int16 -> float
with pytest.warns(UserWarning):
loaded_xr = \
load_utils.load_imgs_from_dir(temp_dir, delimiter='_', dtype="int16")
assert loaded_xr.equals(data_xr)
assert np.issubdtype(loaded_xr.dtype, np.floating)
def test_generate_cell_data_tree_loading():
# is_mibitiff False case, load from directory tree
with tempfile.TemporaryDirectory() as temp_dir:
# define 3 fovs and 3 imgs per fov
fovs, chans = test_utils.gen_fov_chan_names(3, 3)
tiff_dir = os.path.join(temp_dir, "single_channel_inputs")
img_sub_folder = "TIFs"
os.mkdir(tiff_dir)
test_utils.create_paired_xarray_fovs(base_dir=tiff_dir,
fov_names=fovs,
channel_names=chans,
img_shape=(40, 40),
sub_dir=img_sub_folder,
dtype="int16")
# define a subset of fovs
fovs_subset = fovs[:2]
# generate a sample segmentation_mask
cell_mask, _ = test_utils.create_test_extraction_data()
cell_masks = np.zeros((3, 40, 40, 1), dtype="int16")
cell_masks[0, :, :, 0] = cell_mask[0, :, :, 0]
cell_masks[1, 5:, 5:, 0] = cell_mask[0, :-5, :-5, 0]
cell_masks[2, 10:, 10:, 0] = cell_mask[0, :-10, :-10, 0]
segmentation_masks = test_utils.make_labels_xarray(
label_data=cell_masks, compartment_names=['whole_cell'])
with pytest.raises(ValueError):
# specifying fovs not in the original segmentation mask
marker_quantification.generate_cell_data(
segmentation_labels=segmentation_masks.loc[["fov1"]],
tiff_dir=tiff_dir,
img_sub_folder=img_sub_folder,
is_mibitiff=False,
fovs=["fov1", "fov2"],
batch_size=5)
# generate sample norm and arcsinh data for all fovs
norm_data, arcsinh_data = marker_quantification.generate_cell_data(
segmentation_labels=segmentation_masks,
tiff_dir=tiff_dir,
img_sub_folder=img_sub_folder,
is_mibitiff=False,
fovs=None,
batch_size=2)
assert norm_data.shape[0] > 0 and norm_data.shape[1] > 0
assert arcsinh_data.shape[0] > 0 and arcsinh_data.shape[1] > 0
# generate sample norm and arcsinh data for a subset of fovs
norm_data, arcsinh_data = marker_quantification.generate_cell_data(
segmentation_labels=segmentation_masks,
tiff_dir=tiff_dir,
img_sub_folder=img_sub_folder,
is_mibitiff=False,
fovs=fovs_subset,
batch_size=2)
assert norm_data.shape[0] > 0 and norm_data.shape[1] > 0
assert arcsinh_data.shape[0] > 0 and arcsinh_data.shape[1] > 0