Set path in loaded data to PurePath

eitprocessing/datahandling/eitdata.py

@@ -3,7 +3,7 @@
 import warnings
 from dataclasses import InitVar, dataclass, field
 from enum import Enum
-from pathlib import Path
+from pathlib import PurePath
 from typing import TYPE_CHECKING, Any, TypeVar
 
 import numpy as np
@@ -40,7 +40,7 @@ class is meant to hold data from (part of) a singular continuous measurement.
         pixel_impedance: Impedance values for each pixel at each frame.
     """  # TODO: fix docstring
 
-    path: str | Path | list[Path | str] = field(compare=False, repr=False)
+    path: str | PurePath | list[PurePath | str] = field(compare=False, repr=False)
     nframes: int = field(repr=False)
     time: np.ndarray = field(repr=False)
     sample_frequency: float = field(metadata={"check_equivalence": True}, repr=False)
@@ -94,16 +94,16 @@ def framerate(self) -> float:
 
     @staticmethod
     def ensure_path_list(
-        path: str | Path | list[str | Path],
-    ) -> list[Path]:
+        path: str | PurePath | list[str | PurePath],
+    ) -> list[PurePath]:
         """Return the path or paths as a list.
 
-        The path of any EITData object can be a single str/Path or a list of str/Path objects. This method returns a
-        list of Path objects given either a str/Path or list of str/Paths.
+        The path of any EITData object can be a single str/PurePath or a list of str/PurePath objects. This method
+        returns a list of PurePath objects given either a str/PurePath or list of str/PurePaths.
         """
         if isinstance(path, list):
-            return [Path(p) for p in path]
-        return [Path(path)]
+            return [PurePath(p) for p in path]
+        return [PurePath(path)]
 
     def __add__(self: Self, other: Self) -> Self:
         return self.concatenate(other)

eitprocessing/datahandling/loading/__init__.py

@@ -1,13 +1,13 @@
 from functools import reduce
-from pathlib import Path
+from pathlib import Path, PurePath
 
 from eitprocessing.datahandling.datacollection import DataCollection
 from eitprocessing.datahandling.eitdata import EITData, Vendor
 from eitprocessing.datahandling.sequence import Sequence
 
 
 def load_eit_data(
-    path: str | Path | list[str | Path],
+    path: str | PurePath | list[str | PurePath],
     vendor: Vendor | str,
     label: str | None = None,
     name: str | None = None,
@@ -78,7 +78,7 @@ def load_eit_data(
     interval_datasets: list[DataCollection] = []
 
     for single_path in paths:
-        single_path.resolve(strict=True)  # raise error if any file does not exist
+        Path(single_path).resolve(strict=True)  # raise error if any file does not exist
 
     for single_path in paths:
         loaded_data = load_from_single_path(

eitprocessing/datahandling/loading/draeger.py

@@ -5,6 +5,7 @@
 import sys
 import warnings
 from functools import partial
+from pathlib import Path, PurePath
 from typing import TYPE_CHECKING, NamedTuple
 from warnings import catch_warnings
 
@@ -21,8 +22,6 @@
 from eitprocessing.datahandling.sparsedata import SparseData
 
 if TYPE_CHECKING:
-    from pathlib import Path
-
     from numpy.typing import NDArray
 
 load_draeger_data = partial(load_eit_data, vendor=Vendor.DRAEGER)
@@ -31,13 +30,13 @@
 
 
 def load_from_single_path(  # noqa: PLR0915
-    path: Path,
+    path: PurePath,
     sample_frequency: float | None = None,
     first_frame: int = 0,
     max_frames: int | None = None,
 ) -> dict[str, DataCollection]:
     """Load Dräger EIT data from path."""
-    file_size = path.stat().st_size
+    file_size = Path(path).stat().st_size
 
     frame_size: int
     medibus_fields: list
@@ -88,7 +87,7 @@ def load_from_single_path(  # noqa: PLR0915
     phases: list[tuple[float, int]] = []
     medibus_data = np.zeros((len(medibus_fields), n_frames), dtype=np.float32)
 
-    with path.open("br") as fo, mmap.mmap(fo.fileno(), length=0, access=mmap.ACCESS_READ) as fh:
+    with Path(path).open("br") as fo, mmap.mmap(fo.fileno(), length=0, access=mmap.ACCESS_READ) as fh:
         fh.seek(first_frame_to_load * frame_size)
         reader = BinReader(fh)
         previous_marker = None

eitprocessing/datahandling/loading/sentec.py

@@ -5,6 +5,7 @@
 import warnings
 from enum import IntEnum
 from functools import partial
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -18,7 +19,7 @@
 from eitprocessing.datahandling.sparsedata import SparseData
 
 if TYPE_CHECKING:
-    from pathlib import Path
+    from pathlib import PurePath
 
     from numpy.typing import NDArray
 
@@ -28,15 +29,15 @@
 
 
 def load_from_single_path(
-    path: Path,
+    path: PurePath,
     sample_frequency: float | None = None,
     first_frame: int = 0,
     max_frames: int | None = None,
 ) -> dict[str, DataCollection]:
     """Load Sentec EIT data from path."""
     time: list[float] = []
     index = 0
-    with path.open("br") as fo, mmap.mmap(fo.fileno(), length=0, access=mmap.ACCESS_READ) as fh:
+    with Path(path).open("br") as fo, mmap.mmap(fo.fileno(), length=0, access=mmap.ACCESS_READ) as fh:
         file_length = os.fstat(fo.fileno()).st_size
         reader = BinReader(fh, endian="little")
         version = reader.uint8()

eitprocessing/datahandling/loading/timpel.py

@@ -2,6 +2,7 @@
 
 import warnings
 from functools import partial
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -15,7 +16,7 @@
 from eitprocessing.datahandling.sparsedata import SparseData
 
 if TYPE_CHECKING:
-    from pathlib import Path
+    from pathlib import PurePath
 
     from numpy.typing import NDArray
 
@@ -30,7 +31,7 @@
 
 
 def load_from_single_path(
-    path: Path,
+    path: PurePath,
     sample_frequency: float | None = TIMPEL_SAMPLE_FREQUENCY,
     first_frame: int = 0,
     max_frames: int | None = None,
@@ -41,7 +42,7 @@ def load_from_single_path(
 
     try:
         data: NDArray = np.loadtxt(
-            str(path),
+            str(Path(path)),
             dtype=float,
             delimiter=",",
             skiprows=first_frame,

tests/eitdata/test_loading_draeger.py

@@ -1,6 +1,6 @@
 import sys
 import tempfile
-from pathlib import Path
+from pathlib import Path, PurePath
 
 import numpy as np
 import pytest
@@ -80,6 +80,10 @@ def test_load_draeger(
         "Loading without sample frequency should yield the same data"
     )
 
+    path = sequence.eit_data["raw"].path
+    assert isinstance(path, PurePath), "EITData path should be a PurePath object"
+    assert not isinstance(path, Path), "EITData path should be a PurePath object"
+
 
 def test_draeger_20hz_healthy_volunteer_2_differ(
     draeger_20hz_healthy_volunteer: Sequence, draeger_20hz_healthy_volunteer_fixed_rr: Sequence
@@ -187,7 +191,7 @@ def test_event_on_first_frame(draeger_20hz_healthy_volunteer: Sequence):
     with tempfile.NamedTemporaryFile(**kwargs) as temporary_file:
         # Create a temporary file, that is removed after the context manager is closed
         tempfile_path = Path(temporary_file.name)
-        with draeger_20hz_healthy_volunteer.eit_data["raw"].path.open("rb") as original_file:
+        with Path(draeger_20hz_healthy_volunteer.eit_data["raw"].path).open("rb") as original_file:
             original_file.seek(ignore_bytes)  # skip frames before the event
             temporary_file.write(original_file.read())  # write remaining data to temp file
 

tests/eitdata/test_loading_sentec.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from pathlib import Path, PurePath
 
 import numpy as np
 import pytest
@@ -55,6 +55,9 @@ def test_load_sentec_single_file(
         label="something else",
     ), "Loading with a different label should yield same data"
 
+    assert isinstance(sequence.eit_data["raw"].path, PurePath), "EITData path should be a PurePath object"
+    assert not isinstance(sequence.eit_data["raw"].path, Path), "EITData path should be a PurePath object"
+
 
 @pytest.mark.parametrize(
     ("sequence_a_fixture_name", "sequence_b_fixture_name", "sequence_merge_fixture_name"),
@@ -95,6 +98,13 @@ def test_load_sentec_multiple_files(
         "Second part of merged sequence should match second individual sequence"
     )
 
+    assert all(isinstance(path_, PurePath) for path_ in sequence_merged.eit_data["raw"].path), (
+        "EITData path should be a PurePath object"
+    )
+    assert not any(isinstance(path_, Path) for path_ in sequence_merged.eit_data["raw"].path), (
+        "EITData path should not be a Path object"
+    )
+
 
 def test_load_sentec_skip_frames(sentec_healthy_volunteer_1a: Sequence, sentec_healthy_volunteer_1a_path: Path):
     n_frames = len(sentec_healthy_volunteer_1a)

tests/eitdata/test_loading_timpel.py

@@ -1,3 +1,5 @@
+from pathlib import Path, PurePath
+
 import pytest
 
 from eitprocessing.datahandling.eitdata import EITData, Vendor
@@ -25,6 +27,9 @@ def test_loading_timpel(
     loaded_using_enum_vendor = load_eit_data(sequence.eit_data["raw"].path, vendor=Vendor.TIMPEL, label="timpel")
     assert sequence == loaded_using_enum_vendor
 
+    assert isinstance(sequence.eit_data["raw"].path, PurePath), "EITData path should be a PurePath object"
+    assert not isinstance(sequence.eit_data["raw"].path, Path), "EITData path should be a PurePath object"
+
 
 def test_loading_timpel_multiple_files():
     # TODO: find out whether it is possible to have a single measurements split into multiple files