def copy_xml_with_newpath(xml_in,
xml_out,
data_path,
path_type="relative",
data_format=None):
assert path_type in ("absolute", "relative")
if data_format is None:
data_format = get_bdv_format(xml_in)
# get the path node inn the xml tree
root = ET.parse(xml_in).getroot()
seqdesc = root.find("SequenceDescription")
imgload = seqdesc.find("ImageLoader")
imgload.set("format", data_format)
et = imgload.find("hdf5")
if et is None:
et = imgload.find("n5")
if et is None:
raise RuntimeError("Could not find data node")
et.tag = data_format.split(".")[-1]
et.text = data_path
et.set("type", path_type)
indent_xml(root)
tree = ET.ElementTree(root)
tree.write(xml_out)
def get_seg_key_xml(xml_path, scale):
bdv_format = get_bdv_format(xml_path)
if bdv_format == 'bdv.hdf5':
return get_key(True, time_point=0, setup_id=0, scale=scale)
elif bdv_format == 'bdv.n5':
return get_key(False, time_point=0, setup_id=0, scale=scale)
else:
raise RuntimeError("Invalid bdv format: %s" % bdv_format)
def _get_file_format(path):
if not os.path.exists(path):
raise ValueError(f"{path} does not exist.")
elif path.endswith(".xml"):
file_format = bdv_metadata.get_bdv_format(path)
elif path.endswith(".ome.zarr"):
file_format = "ome.zarr"
else:
raise ValueError(f"Could not infer file format from {path}.")
return file_format
def copy_file(xml_in, xml_out, storage='local'):
if storage == 'local':
data_path = get_data_path(xml_in, return_absolute_path=True)
bdv_format = get_bdv_format(xml_in)
xml_dir = os.path.split(xml_out)[0]
data_path = os.path.relpath(data_path, start=xml_dir)
copy_xml_with_newpath(xml_in, xml_out, data_path,
path_type='relative', data_format=bdv_format)
elif storage == 'remote':
shutil.copyfile(xml_in, xml_out)
else:
raise ValueError("Invalid storage spec %s" % storage)
def copy_xml_file(xml_in, xml_out, file_format):
if file_format in ('bdv.hdf5', 'bdv.n5'):
data_path = get_data_path(xml_in, return_absolute_path=True)
bdv_format = get_bdv_format(xml_in)
xml_dir = os.path.split(xml_out)[0]
data_path = os.path.relpath(data_path, start=xml_dir)
copy_xml_with_newpath(xml_in,
xml_out,
data_path,
path_type='relative',
data_format=bdv_format)
elif file_format == 'bdv.n5.s3':
shutil.copyfile(xml_in, xml_out)
else:
raise ValueError(f"Invalid file format {file_format}")
def add_bdv_image(xml_path,
root,
dataset_name,
image_name=None,
file_format="bdv.n5",
menu_name=None,
scale_factors=None,
tmp_folder=None,
target="local",
max_jobs=multiprocessing.cpu_count(),
is_default_dataset=False,
description=None,
trafos_for_mobie=None,
move_data=False,
int_to_uint=False):
"""Add the image(s) specified in an bdv xml file and copy the metadata.
"""
# find how many timepoints we have
t_start, t_stop = bdv_metadata.get_time_range(xml_path)
if t_stop > t_start:
raise NotImplementedError(
"Only a single timepoint is currently supported.")
# get the setup ids and check that image_name is compatible
setup_ids = bdv_metadata.get_setup_ids(xml_path)
if image_name is None:
image_name = [None] * len(setup_ids)
else:
if isinstance(image_name, str):
image_name = [image_name]
assert len(image_name) == len(setup_ids)
data_path = bdv_metadata.get_data_path(xml_path, return_absolute_path=True)
# get the key for the input data format
input_format = bdv_metadata.get_bdv_format(xml_path)
move_only = False
if move_data:
if input_format == file_format:
move_only = True
else:
print(
"Different input format than target format. Will convert data instead of moving it."
)
if len(setup_ids) > 1:
move_only = False
print(
"Cannot move XML with multiple setups. Will convert data instead of moving it."
)
for setup_id, name in zip(setup_ids, image_name):
input_key = get_key(input_format == "bdv.hdf5",
timepoint=t_start,
setup_id=setup_id,
scale=0)
# get the resolution, scale_factors, chunks and unit
resolution = bdv_metadata.get_resolution(xml_path, setup_id)
if scale_factors is None:
scale_factors = get_scale_factors(data_path, setup_id)
scale_factors = absolute_to_relative_scale_factors(
scale_factors)[1:]
with open_file(data_path, "r") as f:
chunks = f[input_key].chunks
unit = bdv_metadata.get_unit(xml_path, setup_id)
# get the name of this source
if name is None:
name = bdv_metadata.get_name(xml_path, setup_id)
# get the view (=MoBIE metadata) and transformation (=bdv metadata)
# from the input bdv metadata
view, transformation = _view_and_trafo_from_xml(
xml_path, setup_id, t_start, name, menu_name, trafos_for_mobie)
tmp_folder_ = None if tmp_folder is None else f"{tmp_folder}_{name}"
add_image(data_path,
input_key,
root,
dataset_name,
image_name=name,
resolution=resolution,
scale_factors=scale_factors,
chunks=chunks,
file_format=file_format,
menu_name=menu_name,
tmp_folder=tmp_folder_,
target=target,
max_jobs=max_jobs,
unit=unit,
view=view,
transformation=transformation,
is_default_dataset=is_default_dataset,
description=description,
move_only=move_only,
int_to_uint=int_to_uint)