Parse philips tiff mettadata #80
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Thanks @erikogabrielsson for your contribution! I tested locally with a few philips tiff files. Looks good! |
kaczmarj
reviewed
Nov 30, 2023
| 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,
kaczmarj
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Nov 30, 2023
According to the DICOM spec, the first value is row mpp and second is column mpp. > Physical distance in the imaging target (patient, specimen, or phantom) between the centers of each pixel, specified by a numeric pair - adjacent row spacing (delimiter) adjacent column spacing in mm. See Section 10.7.1.3 for further explanation of the value order. source: https://dicom.innolitics.com/ciods/vl-whole-slide-microscopy-image/vl-whole-slide-microscopy-image-multi-frame-functional-groups/52009230/00289110/00280030 Related to Bayer-Group#80 (review)
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Fix for #77
Took inspiration from the philps tiff metadata parser from OpenTile.
Not sure how to write a good test for this without a test file? Got this from the file I had locally available: