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Merge 4424963 into dcc6338
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@camisowers
camisowers authored Nov 1, 2022
2 parents dcc6338 + 4424963 commit 1a62080
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Showing 3 changed files with 77 additions and 16 deletions.
4 changes: 2 additions & 2 deletions ark/utils/data_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -636,11 +636,11 @@ def stitch_images_by_shape(data_dir, stitched_dir, img_sub_folder=None, channels
os.makedirs(stitched_dir)

file_ext = channel_imgs[0].split('.')[1]
_, num_rows, num_cols = load_utils.get_tiled_fov_names(fovs, return_dims=True)
expected_fovs, num_rows, num_cols = load_utils.get_tiled_fov_names(fovs, return_dims=True)

# save new images to the stitched_images, one channel at a time
for chan in channels:
image_data = load_tiled_img_data(data_dir, fovs, chan,
image_data = load_tiled_img_data(data_dir, fovs, expected_fovs, chan,
single_dir=any([segmentation, clustering]),
file_ext=file_ext, img_sub_folder=img_sub_folder)
stitched_data = stitch_images(image_data, num_cols)
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28 changes: 22 additions & 6 deletions ark/utils/load_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -394,15 +394,17 @@ def get_tiled_fov_names(fov_list, return_dims=False):
return expected_fovs


def load_tiled_img_data(data_dir, fov_list, channel, single_dir, file_ext='tiff',
def load_tiled_img_data(data_dir, fovs, expected_fovs, channel, single_dir, file_ext='tiff',
img_sub_folder=''):
"""Takes a set of images from a directory structure and loads them into a tiled xarray.
Args:
data_dir (str):
directory containing folders of images
fov_list (list):
list of fovs to load data for
fovs (list/dict):
list of fovs (or dictionary with folder and RnCm names) to load data for
expected_fovs (list):
list of all expected RnCm fovs names in the tiled grid
channel (str):
single image name to load
single_dir (bool):
Expand All @@ -419,7 +421,13 @@ def load_tiled_img_data(data_dir, fov_list, channel, single_dir, file_ext='tiff'

iou.validate_paths(data_dir, data_prefix=False)

expected_fovs = get_tiled_fov_names(fov_list)
# check for toffy fovs
if type(fovs) is dict:
fov_list = list(fovs.values())
tiled_names = list(fovs.keys())
else:
fov_list = fovs
tiled_names = []

# no missing fov images, load data normally and return array
if len(fov_list) == len(expected_fovs):
Expand All @@ -445,14 +453,22 @@ def load_tiled_img_data(data_dir, fov_list, channel, single_dir, file_ext='tiff'
# load in fov data for images, leave missing fovs as zeros
if fov_name in fov_list:
if single_dir:
temp_img = io.imread(os.path.join(data_dir, expected_fovs[fov] + '_' +
temp_img = io.imread(os.path.join(data_dir, fov_name + '_' +
channel + '.' + file_ext))
else:
temp_img = io.imread(os.path.join(data_dir, expected_fovs[fov], img_sub_folder,
temp_img = io.imread(os.path.join(data_dir, fov_name, img_sub_folder,
channel + '.' + file_ext))
# fill in specific spot in array
img_data[fov, :temp_img.shape[0], :temp_img.shape[1], 0] = temp_img

# check against tiled_names from dict for toffy dirs
elif fov_name in tiled_names:
folder_name = fovs[fov_name]
temp_img = io.imread(os.path.join(data_dir, folder_name, img_sub_folder,
channel + '.' + file_ext))
# fill in specific spot in array
img_data[fov, :temp_img.shape[0], :temp_img.shape[1], 0] = temp_img

# check to make sure that dtype wasn't too small for range of data
if np.min(img_data) < 0:
warnings.warn("You have images with negative values loaded in.")
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61 changes: 53 additions & 8 deletions ark/utils/load_utils_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -359,7 +359,7 @@ def test_get_tiled_fov_names():
def test_load_tiled_img_data(single_dir, img_sub_folder):
# invalid directory is provided
with pytest.raises(FileNotFoundError):
loaded_xr = load_utils.load_tiled_img_data('not_a_dir', [], 'chan1',
loaded_xr = load_utils.load_tiled_img_data('not_a_dir', [], [], 'chan1',
single_dir=False,)

# check with no missing FOVS
Expand All @@ -372,13 +372,33 @@ def test_load_tiled_img_data(single_dir, img_sub_folder):
)

# check default loading of chan1 images
loaded_xr = load_utils.load_tiled_img_data(temp_dir, fovs, 'chan1',
single_dir=single_dir,
loaded_xr = load_utils.load_tiled_img_data(temp_dir, fovs, expected_fovs=fovs,
channel='chan1', single_dir=single_dir,
img_sub_folder=img_sub_folder)

assert loaded_xr.equals(data_xr[:, :, :, :-1])
assert loaded_xr.shape == (3, 10, 10, 1)

# check toffy dict loading
if not single_dir:
toffy_fovs = {'R1C1': 'fov-1', 'R1C2': 'fov-3', 'R1C3': 'fov-2'}
fovs = list(toffy_fovs.values())
expected_fovs = load_utils.get_tiled_fov_names(list(toffy_fovs.keys()))

filelocs, data_xr = test_utils.create_paired_xarray_fovs(
temp_dir, fovs, ['chan1', 'chan2'], img_shape=(10, 10), fills=True,
sub_dir=img_sub_folder, dtype="int16", single_dir=single_dir
)

# check default loading of chan1 images
loaded_xr = load_utils.load_tiled_img_data(temp_dir, toffy_fovs,
expected_fovs=expected_fovs,
channel='chan1', single_dir=single_dir,
img_sub_folder=img_sub_folder)

assert loaded_xr.equals(data_xr[:, :, :, :-1])
assert loaded_xr.shape == (3, 10, 10, 1)

# check loading with missing FOV images
with tempfile.TemporaryDirectory() as temp_dir:

Expand All @@ -396,12 +416,37 @@ def test_load_tiled_img_data(single_dir, img_sub_folder):

# check successful loading for one channel
loaded_xr = \
load_utils.load_tiled_img_data(temp_dir, ['R1C1', 'R1C2', 'R2C2'], 'chan1',
load_utils.load_tiled_img_data(temp_dir, ['R1C1', 'R1C2', 'R2C2'], fovs, 'chan1',
single_dir=single_dir, img_sub_folder=img_sub_folder)

assert loaded_xr.equals(data_xr[:, :, :, :-1])
assert loaded_xr.shape == (4, 10, 10, 1)

# check toffy dict loading
if not single_dir:
toffy_fovs = {'R1C1': 'fov-3', 'R1C2': 'fov-1', 'R2C1': 'fov-4', 'R2C2': 'fov-2'}
fovs = list(toffy_fovs.values())
expected_fovs = load_utils.get_tiled_fov_names(list(toffy_fovs.keys()))

filelocs, data_xr = test_utils.create_paired_xarray_fovs(
temp_dir, fovs, ['chan1', 'chan2'], img_shape=(10, 10), delimiter='_', fills=True,
sub_dir=img_sub_folder, dtype="int16", single_dir=single_dir
)
data_xr['fovs'] = list(toffy_fovs.keys())

# remove images and expected data for one fov
data_xr[2, :, :, :] = np.zeros((10, 10, 1), dtype='int16')
shutil.rmtree(os.path.join(temp_dir, 'fov-4'))
toffy_fovs.pop('R2C1')

# check successful loading for one channel
loaded_xr = \
load_utils.load_tiled_img_data(temp_dir, toffy_fovs, expected_fovs,
'chan1', single_dir=single_dir,
img_sub_folder=img_sub_folder)

assert loaded_xr.equals(data_xr[:, :, :, :-1])
assert loaded_xr.shape == (4, 10, 10, 1)

# test loading with data_xr containing float values
with tempfile.TemporaryDirectory() as temp_dir:

Expand All @@ -417,8 +462,8 @@ def test_load_tiled_img_data(single_dir, img_sub_folder):
else:
shutil.rmtree(os.path.join(temp_dir, 'R2C1'))

loaded_xr = load_utils.load_tiled_img_data(temp_dir, ['R1C1', 'R1C2', 'R2C2'], 'chan1',
single_dir=single_dir,
loaded_xr = load_utils.load_tiled_img_data(temp_dir, ['R1C1', 'R1C2', 'R2C2'], fovs,
'chan1', single_dir=single_dir,
img_sub_folder=img_sub_folder)
assert loaded_xr.shape == (4, 10, 10, 1)
assert np.issubdtype(loaded_xr.dtype, np.floating)
Expand All @@ -440,7 +485,7 @@ def test_load_tiled_img_data(single_dir, img_sub_folder):

loaded_xr = \
load_utils.load_tiled_img_data(temp_dir, ['run_1_R1C1', 'run_1_R1C2', 'run_2_R2C2'],
'chan1', single_dir=single_dir,
fovs, 'chan1', single_dir=single_dir,
img_sub_folder=img_sub_folder)
assert loaded_xr.equals(data_xr)
assert loaded_xr.shape == (4, 10, 10, 1)

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