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import sys
from argparse import ArgumentParser
from pathlib import Path
from typing import Union
import h5py
from .utils import progress_bar
__all__ = ["copy_structure"]
def progress(processed, total, *, show=True):
"""Show progress information"""
if not show:
return
pbar = progress_bar(processed, total)
if sys.stderr.isatty():
# "\x1b[2K": delete whole line, "\x1b[1A": move up cursor
print("\x1b[2K\x1b[1A\x1b[2K\x1b[1A", file=sys.stderr)
print(pbar, file=sys.stderr)
class Cloner:
def __init__(self, input, output, *, run_data=False, control_data=False):
self.run_data = run_data
self.control_data = control_data
self.visited = {}
if output.file.mode == "r":
raise ValueError("Output file must be writeable.")
self.visit(input, output)
@staticmethod
def _copy_attrs(input, output):
for key, value in input.attrs.items():
output.attrs.create(key, value)
def visit(self, obj, output):
if obj.name != "/":
link = obj.file.get(obj.name, getlink=True)
if isinstance(link, h5py.SoftLink):
# note this works only for SoftLinks. ExternalLink object's
# name is not the name of the path, but the targeted file's path
output[obj.name] = link
return
obj_id = h5py.h5o.get_info(obj.id).addr
if obj_id in self.visited:
# Hardlink to an object we've already seen
output[obj.name] = output[self.visited[obj_id]]
return
self.visited[obj_id] = obj.name
if isinstance(obj, h5py.Dataset):
if (
obj.name.startswith("/INSTRUMENT")
or (obj.name.startswith("/CONTROL") and not self.control_data)
or (obj.name.startswith("/RUN") and not self.run_data)
):
output_obj = output.create_dataset_like(obj.name, obj)
else:
# note: consider using h5py.File.copy once a bug causing
# segfault for dataset with attributes is fixed,
# see: https://github.com/HDFGroup/hdf5/issues/2414
output_obj = output.create_dataset_like(obj.name, obj, data=obj[()])
self._copy_attrs(obj, output_obj)
elif isinstance(obj, h5py.Group):
if obj == obj.file:
# root object
output_obj = output["/"]
else:
output_obj = output.create_group(obj.name)
self._copy_attrs(obj, output_obj)
for name, child in obj.items():
if child.file != obj.file:
# external link
output[f'{obj.name}/{name}'] = obj.get(name, getlink=True)
else:
self.visit(child, output)
else:
# unknown type
return
def copy_structure(
input: Union[Path, str],
output: Union[Path, str],
*,
run_data=False,
control_data=False,
term_progress=False,
) -> None:
"""Clone EuXFEL HDF5 file structure without any of its data.
Clone the input file or files present the input directory.
The cloned files will be written to output.
args:
run_data: Copy data in RUN group if set to True
control_data: Copy data in CONTROL group if set to True
term_progress: show progress in terminal if set to True
"""
if isinstance(input, str):
input = Path(input)
input = input.expanduser()
if isinstance(output, str):
output = Path(output)
output = output.expanduser()
if not output.is_dir():
raise ValueError(f"The given output directory does not exist: {output}")
if h5py.is_hdf5(input):
if output == input.parent:
raise ValueError("Input and output must be different directories.")
Cloner(
h5py.File(input),
h5py.File(output / input.name, "w"),
run_data=run_data,
control_data=control_data,
)
elif input.is_dir():
if output == input:
raise ValueError("Input and output must be different directories.")
# clone all hdf5 file present in the given directory
h5files = [f for f in input.glob("*") if h5py.is_hdf5(f)]
progress(0, len(h5files), show=term_progress)
for n, file_ in enumerate(h5files, start=1):
Cloner(
h5py.File(file_),
h5py.File(output / file_.name, "w"),
run_data=run_data,
control_data=control_data,
)
progress(n, len(h5files), show=term_progress)
else:
raise ValueError(f"invalid input: {input}")
def main(argv=None):
ap = ArgumentParser("Clone EuXFEL HDF5 files but with empty datasets.")
ap.add_argument("input", type=str, help="Path to an HDF5 file or a directory.")
ap.add_argument(
"output", type=str, help="Output directory to write the cloned files."
)
ap.add_argument(
"--copy-run-data",
"-cr",
action="store_true",
default=False,
help="Copy data present in the RUN group.",
)
ap.add_argument(
"--copy-control-data",
"-cc",
action="store_true",
default=False,
help="Copy data present in the CONTROL group.",
)
args = ap.parse_args(argv)
print(f"Cloning file(s) structure:\ninput: {args.input}\nOutput: {args.output}\n")
copy_structure(
args.input,
args.output,
run_data=args.copy_run_data,
control_data=args.copy_control_data,
term_progress=True,
)
print("Done.")
if __name__ == "__main__":
main(sys.argv[1:])
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