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fix pre-commit benchmark_image
1 parent 93554e7 commit 5a20f41

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+8
-5
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-5
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benchmarks/benchmark_image.py

Lines changed: 8 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -6,11 +6,12 @@
66

77
import shutil
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from pathlib import Path
9+
from typing import Any
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1011
from spatialdata import SpatialData
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from xarray import DataArray
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13-
from spatialdata_io import image # type: ignore[attr-defined]
14+
from spatialdata_io import image
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# =============================================================================
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# CONFIGURATION - Edit these paths to match your setup
@@ -50,13 +51,15 @@ class IOBenchmarkImage:
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]
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param_names = ["scale_factors", "use_tiff_memmap", "chunks"]
5253

53-
def setup(self, *_) -> None:
54+
def setup(self, *_: Any) -> None:
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"""Set up paths for benchmarking."""
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self.path_read, self.path_write = get_paths()
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if self.path_write.exists():
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shutil.rmtree(self.path_write)
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59-
def _convert_image(self, scale_factors, use_tiff_memmap, chunks) -> SpatialData:
60+
def _convert_image(
61+
self, scale_factors: list[int] | None, use_tiff_memmap: bool, chunks: tuple[int, int]
62+
) -> SpatialData:
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"""Read image data with specified parameters."""
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im = image(
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input=self.path_read,
@@ -79,12 +82,12 @@ def _convert_image(self, scale_factors, use_tiff_memmap, chunks) -> SpatialData:
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assert sdata["image"].chunksizes["y"] == chunks[1]
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return sdata
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82-
def time_io(self, scale_factors, use_tiff_memmap, chunks) -> None:
85+
def time_io(self, scale_factors: list[int] | None, use_tiff_memmap: bool, chunks: tuple[int, int]) -> None:
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"""Walltime for data parsing."""
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sdata = self._convert_image(scale_factors, use_tiff_memmap, chunks)
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sdata.write(self.path_write)
8689

87-
def peakmem_io(self, scale_factors, use_tiff_memmap, chunks) -> None:
90+
def peakmem_io(self, scale_factors: list[int] | None, use_tiff_memmap: bool, chunks: tuple[int, int]) -> None:
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"""Peak memory for data parsing."""
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sdata = self._convert_image(scale_factors, use_tiff_memmap, chunks)
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sdata.write(self.path_write)

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