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Parse philips tiff mettadata #80

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merged 2 commits into from
Nov 29, 2023
Merged

Parse philips tiff mettadata #80

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e44b8ba
Parse philips tiff mettadata
erikogabrielsson Nov 29, 2023
93f9e25
Remove unused import
erikogabrielsson Nov 29, 2023
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33 changes: 33 additions & 0 deletions tiffslide/tiffslide.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from typing import Iterator
from typing import Literal
from typing import Mapping
from typing import Optional
from typing import TypeVar
from typing import overload
from warnings import warn
Expand Down Expand Up @@ -644,6 +645,7 @@ class _PropertyParser:
scn="leica",
bif="ventana",
ndpi="hamamatsu",
philips="philips_tiff"
# add more when needed
)

Expand Down Expand Up @@ -843,6 +845,37 @@ def parse_generic_tiff(self) -> dict[str, Any]:
md.update(self.collect_level_info(series0))
return md

def parse_philips_tiff(self) -> dict[str, Any]:
"""parse Philips tiff properties"""
md = self.parse_generic_tiff()
if self._tf.philips_metadata is None:
return md
philips_metadata = ElementTree.fromstring(self._tf.philips_metadata)
def get_first_attribute_with_name(
root: ElementTree.Element,
name: str
) -> Optional[str]:
return next(
root.iterfind(f".//Attribute[@Name='{name}']")
).text
md[PROPERTY_NAME_VENDOR] = get_first_attribute_with_name(
philips_metadata,
'DICOM_MANUFACTURER'
)
pixel_spacing_attribute = get_first_attribute_with_name(
philips_metadata,
'DICOM_PIXEL_SPACING'
)
if pixel_spacing_attribute is not None:
pixel_spacings = [
float(element.strip('"')) * 1000
for element in pixel_spacing_attribute.split(' ')
]
mpp_x, mpp_y = pixel_spacings[0], pixel_spacings[1]
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@erikogabrielsson @ap-- i think x and y need to be reversed here. openslide's website says the following:

openslide.mpp-x
    calculated as 1000 * philips.DICOM_PIXEL_SPACING[1]
openslide.mpp-y
    calculated as 1000 * philips.DICOM_PIXEL_SPACING[0]

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You are correct. Per DICOM specifications the first value is the row spacing and the second value the column spacing,

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i submitted a fix in #81

md[PROPERTY_NAME_MPP_X] = mpp_x
md[PROPERTY_NAME_MPP_Y] = mpp_y
return md


def _parse_metadata_aperio(desc: str) -> dict[str, Any]:
"""Aperio SVS metadata"""
Expand Down
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