synapse_net.tools.volume_reader 

 1import os
 2from typing import Callable, List, Optional, Sequence, Union
 3
 4from elf.io import open_file, is_dataset
 5from napari.types import LayerData
 6from synapse_net.file_utils import read_mrc
 7
 8
 9PathLike = str
10PathOrPaths = Union[PathLike, Sequence[PathLike]]
11ReaderFunction = Callable[[PathOrPaths], List[LayerData]]
12
13
14def get_reader(path: PathOrPaths) -> Optional[ReaderFunction]:
15    # If we recognize the format, we return the actual reader function.
16    if isinstance(path, str) and path.endswith((".mrc", ".rec", ".h5")):
17        return read_image_volume
18    # Otherwise we return None.
19    return None
20
21
22def _read_mrc(path, fname):
23    data, voxel_size = read_mrc(path)
24    metadata = {"file_path": path, "voxel_size": voxel_size}
25    layer_attributes = {
26        "name": fname,
27        "colormap": "gray",
28        "metadata": metadata
29    }
30    return [(data, layer_attributes)]
31
32
33# For hdf5 files we read the full content.
34def _read_hdf5(path):
35    return_data = []
36
37    def visitor(name, obj):
38        if is_dataset(obj):
39            data = obj[:]
40            attributes = {"name": name}
41            if str(data.dtype) in ("int32", "uint32", "int64", "uint64"):
42                layer_type = "labels"
43            else:
44                layer_type = "image"
45                attributes["colormap"] = "gray"
46
47            return_data.append((data, attributes, layer_type))
48
49    with open_file(path, mode="r") as f:
50        f.visititems(visitor)
51
52    return return_data
53
54
55def read_image_volume(path: PathOrPaths) -> List[LayerData]:
56    fname = os.path.basename(path)
57    fname, ext = os.path.splitext(fname)
58
59    try:
60        if ext in (".mrc", ".rec"):
61            return _read_mrc(path, fname)
62        else:   # This is an hdf5 file
63            return _read_hdf5(path)
64
65    except Exception as e:
66        print(f"Failed to read file: {e}")
67        return
PathLike = <class 'str'>
PathOrPaths = typing.Union[str, typing.Sequence[str]]
ReaderFunction = typing.Callable[[typing.Union[str, typing.Sequence[str]]], typing.List[typing.Union[tuple[typing.Any], tuple[typing.Any, collections.abc.Mapping], tuple[typing.Any, collections.abc.Mapping, typing.Literal['graph', 'image', 'labels', 'points', 'shapes', 'surface', 'tracks', 'vectors']]]]]
def get_reader( path: Union[str, Sequence[str]]) -> Optional[Callable[[Union[str, Sequence[str]]], List[Union[tuple[Any], tuple[Any, Mapping], tuple[Any, Mapping, Literal['graph', 'image', 'labels', 'points', 'shapes', 'surface', 'tracks', 'vectors']]]]]]: 
15def get_reader(path: PathOrPaths) -> Optional[ReaderFunction]:
16    # If we recognize the format, we return the actual reader function.
17    if isinstance(path, str) and path.endswith((".mrc", ".rec", ".h5")):
18        return read_image_volume
19    # Otherwise we return None.
20    return None
def read_image_volume( path: Union[str, Sequence[str]]) -> List[Union[tuple[Any], tuple[Any, Mapping], tuple[Any, Mapping, Literal['graph', 'image', 'labels', 'points', 'shapes', 'surface', 'tracks', 'vectors']]]]: 
56def read_image_volume(path: PathOrPaths) -> List[LayerData]:
57    fname = os.path.basename(path)
58    fname, ext = os.path.splitext(fname)
59
60    try:
61        if ext in (".mrc", ".rec"):
62            return _read_mrc(path, fname)
63        else:   # This is an hdf5 file
64            return _read_hdf5(path)
65
66    except Exception as e:
67        print(f"Failed to read file: {e}")
68        return