def data_dir():
cp_dir = Path.home().joinpath('.cellpose')
data_dir = cp_dir.joinpath('data')
data_dir.mkdir(exist_ok=True)
data_dir_2D = data_dir.joinpath('2D')
data_dir_2D.mkdir(exist_ok=True)
data_dir_3D = data_dir.joinpath('3D')
data_dir_3D.mkdir(exist_ok=True)
for image_name in image_names:
url = 'http://www.cellpose.org/static/data/' + image_name
parts = urlparse(url)
if '2D' in image_name:
cached_file = str(data_dir_2D.joinpath(image_name).resolve())
else:
cached_file = str(data_dir_3D.joinpath(image_name).resolve())
if not os.path.exists(cached_file):
sys.stderr.write('Downloading: "{}" to {}\n'.format(url, cached_file))
# check if mask downloaded (and clear potential previous test data)
name, ext = os.path.splitext(cached_file)
mask_file = name + '_cp_masks' + ext
if os.path.exists(mask_file):
os.remove(mask_file)
cached_mask_file = name + '_masks' + ext
url = 'http://www.cellpose.org/static/data/' + os.path.split(cached_mask_file)[-1]
if not os.path.exists(cached_mask_file):
utils.download_url_to_file(url, cached_mask_file, progress=True)
return data_dir
def data_dir(image_names):
cp_dir = Path.home().joinpath('.cellpose')
cp_dir.mkdir(exist_ok=True)
data_dir = cp_dir.joinpath('data')
data_dir.mkdir(exist_ok=True)
data_dir_2D = data_dir.joinpath('2D')
data_dir_2D.mkdir(exist_ok=True)
data_dir_3D = data_dir.joinpath('3D')
data_dir_3D.mkdir(exist_ok=True)
data_dir_distributed = data_dir.joinpath('distributed')
data_dir_distributed.mkdir(exist_ok=True)
for i, image_name in enumerate(image_names):
url = 'http://www.cellpose.org/static/data/' + image_name
if i < 3:
cached_file = str(data_dir_2D.joinpath(image_name))
ext = '.png'
elif i < 5:
cached_file = str(data_dir_3D.joinpath(image_name))
ext = '.tif'
else:
cached_file = str(data_dir_distributed.joinpath(image_name))
ext = '.tif'
if not os.path.exists(cached_file):
utils.download_url_to_file(url, cached_file)
# check if mask downloaded (and clear potential previous test data)
if i < 2:
train_dir = data_dir_2D.joinpath('train')
train_dir.mkdir(exist_ok=True)
shutil.copyfile(cached_file, train_dir.joinpath(image_name))
if i < 5:
name = os.path.splitext(cached_file)[0]
mask_file = name + '_cp_masks' + ext
if os.path.exists(mask_file):
os.remove(mask_file)
cached_mask_files = [
name + '_cyto_masks' + ext, name + '_nuclei_masks' + ext
]
for c, cached_mask_file in enumerate(cached_mask_files):
url = 'http://www.cellpose.org/static/data/' + os.path.split(
cached_mask_file)[-1]
if not os.path.exists(cached_mask_file):
print(cached_mask_file)
utils.download_url_to_file(url,
cached_mask_file,
progress=True)
if i < 2 and c == 0:
shutil.copyfile(
cached_mask_file,
train_dir.joinpath(
os.path.splitext(image_name)[0] + '_cyto_masks' +
ext))
return data_dir