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only use specified backend (or tifffile) to read mpp #227

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merged 1 commit into from
Jul 11, 2024
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only use specified backend (or tifffile) to read mpp #227

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14 changes: 10 additions & 4 deletions wsinfer/wsi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,6 +192,8 @@ def _get_mpp_tiffslide(
slide_path: str | Path,
) -> tuple[float, float]:
"""Read MPP using TiffSlide."""
logger.debug("Attempting to read MPP using TiffSlide")

if not HAS_TIFFSLIDE:
logger.critical(
"Cannot read MPP with TiffSlide because TiffSlide is not available"
Expand Down Expand Up @@ -223,6 +225,7 @@ def _get_mpp_tiffslide(
# https://github.com/bayer-science-for-a-better-life/tiffslide/blob/8bea5a4c8e1429071ade6d4c40169ce153786d19/tiffslide/tiffslide.py#L712-L745
def _get_mpp_tifffile(slide_path: str | Path) -> tuple[float, float]:
"""Read MPP using Tifffile."""
logger.debug("Attempting to read MPP using tifffile")
with tifffile.TiffFile(slide_path) as tif:
series0 = tif.series[0]
page0 = series0[0]
Expand Down Expand Up @@ -267,20 +270,23 @@ def get_avg_mpp(slide_path: Path | str) -> float:
mppx: float
mppy: float

if HAS_OPENSLIDE:
if _BACKEND == "openslide":
try:
mppx, mppy = _get_mpp_openslide(slide_path)
return (mppx + mppy) / 2
except CannotReadSpacing:
# At this point, we want to continue to other implementations.
pass
if HAS_TIFFSLIDE:
if _BACKEND == "tiffslide":
try:
mppx, mppy = _get_mpp_tiffslide(slide_path)
return (mppx + mppy) / 2
except CannotReadSpacing:
# Our last hope to read the mpp is tifffile.
pass

logger.debug(f"Failed to read MPP using {_BACKEND}.")
logger.debug("Trying to read MPP with tifffile as last resort.")

# If tiffslide/openslide don't work, try tifffile.
try:
mppx, mppy = _get_mpp_tifffile(slide_path)
return (mppx + mppy) / 2
Expand Down
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