Image Resolution wrongly read in TIFFWSIReader

[rogertrullo]

• TIA Toolbox version: 1.2.1
• Python version: 3.8
• Operating System:

Description

According to the Tiff description, the tags XResolution and YResolution are of type rational. Meaning that we should compute the fraction. In the code:

tiatoolbox/tiatoolbox/wsicore/wsireader.py

Lines 3245 to 3248 in b3ace85

	mpp = [
	utils.misc.ppu2mpp(res_x.value[0], res_units.value),
	utils.misc.ppu2mpp(res_y.value[0], res_units.value),
	]

we are only passing the first element. Instead we should pass res_x.value[0]/res_x.value[1] and res_y.value[0]/res_y.value[0]

[rogertrullo]

I am also having some issues when reading at different pyramid levels:
I think (but I am not sure) that these lines:

tiatoolbox/tiatoolbox/wsicore/wsireader.py

Lines 3505 to 3521 in b3ace85

	# Find parameters for optimal read
	(
	read_level,
	_,
	_,
	post_read_scale,
	baseline_read_size,
	) = self.find_read_rect_params(
	location=location,
	size=size,
	resolution=resolution,
	units=units,
	)
	bounds = utils.transforms.locsize2bounds(
	location=location, size=baseline_read_size
	)

should look like this (use level location and size instead of baseline)

        (
            read_level,
            level_location,
            level_size,
            post_read_scale,
            baseline_read_size,
        ) = self.find_read_rect_params(
            location=location,
            size=size,
            resolution=resolution,
            units=units,
        )

        bounds = utils.transforms.locsize2bounds(
            location=level_location, size=level_size
        )

[shaneahmed]

I am also having some issues when reading at different pyramid levels: I think (but I am not sure) that these lines:

tiatoolbox/tiatoolbox/wsicore/wsireader.py

Lines 3505 to 3521 in b3ace85

	# Find parameters for optimal read
	(
	read_level,
	_,
	_,
	post_read_scale,
	baseline_read_size,
	) = self.find_read_rect_params(
	location=location,
	size=size,
	resolution=resolution,
	units=units,
	)
	bounds = utils.transforms.locsize2bounds(
	location=location, size=baseline_read_size
	)

should look like this (use level location and size instead of baseline)

        (
            read_level,
            level_location,
            level_size,
            post_read_scale,
            baseline_read_size,
        ) = self.find_read_rect_params(
            location=location,
            size=size,
            resolution=resolution,
            units=units,
        )

        bounds = utils.transforms.locsize2bounds(
            location=level_location, size=level_size
        )

@rogertrullo Please can you explain these issues?

[shaneahmed]

Keeping this issue open to address this comment #452 (comment)

[rogertrullo]

@shaneahmed , @John-P , when reading at a different resolution other than the baseline, I have some errors. For example, when reading CMU-1-SMALL-REGION (which I converted to ome.tiff using bioformats2raw and raw2ometiff ) thumbnail

imghe=TIFFWSIReader(path_img)
he_lr = imghe.slide_thumbnail(resolution=5, units="mpp")

I get an img like this:

reading at baseline resolution is fine:

w,h=imghe.info.as_dict()['slide_dimensions']
he_hr=imghe.read_rect((0,0),(w,h))

I think the issue is coming from the fact that we are using location and size at baseline resolution instead of the resolution given by find_read_rect_params

[rogertrullo]

@John-P @shaneahmed , another small issue I have seen, is that when reading metadata in here:

tiatoolbox/tiatoolbox/wsicore/wsireader.py

Lines 3291 to 3296 in b0d5981

	if self.tiff.is_svs:
	filetype_params = self._parse_svs_metadata()
	if self.tiff.is_ome:
	filetype_params = self._parse_ome_metadata()
	if self.tiff.pages[0].is_tiled:
	filetype_params = self._parse_generic_tiled_metadata()

for an ome.tiff file self.tiff.is_ome and self.tiff.pages[0].is_tiled are both True. Since we are checking only with if and not with elif some metadata read by self._parse_ome_metadata() will be overwritten by self._parse_generic_tiled_metadata() making for example objective_power to be None

[jessecanada]

Also having an issue with TIFFWSIReader. Certain ome.tiff when read has array shape (H, W, C), while others are in (C, H, W). This throws off your code. I suggest adding a line in there to make sure the array is always channel-last (or channel-first, whichever you prefer).

[John-P]

@jessecanada Hi, I'd like to look into this for you. Are you able to provide a test image?