Open alevangel opened 2 months ago
I think you can do this with a combination of the getMetadata
and convertRegionScale
methods of tilesource.
The lead developer is away on leave but can respond when he returns.
@cooperlab using getMetadata
, I can only obtain information about the Whole Slide Image at the highest resolution level. However, I would also like to retrieve the shapes of other resolution levels.
I understand. Given the size and resolution of the native level, convertRegionScale can translate the "region" of the whole slide to other resolutions which would give you the corresponding size. large_image provides more flexibility in reading at off-level magnifications but it does complicate things a bit. I just wanted to provide a hint until @manthey can reply in case you need a quick solution.
@cooperlab , very appreciated. Could you provide me with some example code? I can’t figure out how to implement it.
I have attempted the following solution to address the problem at hand.
I am awaiting a response from @manthey to determine if there is a more robust solution available.
def _correct_level(self, level: int):
max_level = self.slide.levels - 1
# Large Image levels are in the opposite order of OpenSlide levels
return max_level - level
def get_image_shape(self, level: int = 0):
level = self._correct_level(level)
# get magnification for level
mag = self.slide.getMagnificationForLevel(level)
metadata = self.slide.metadata
left, top, right, bottom = self.slide._getRegionBounds(
metadata, desiredMagnification=mag)
regionWidth = right - left
regionHeight = bottom - top
if mag.get('scale') in (1.0, None):
maxWidth, maxHeight = regionWidth, regionHeight
else:
maxWidth = regionWidth / cast(float, mag['scale'])
maxHeight = regionHeight / cast(float, mag['scale'])
outWidth, outHeight, calcScale = large_image.tilesource.utilities._calculateWidthHeight(
maxWidth, maxHeight, regionWidth, regionHeight)
return outHeight, outWidth
I adapted the code provided here:
@alevangel you can also use the result of getMetadata
to define a region that is the entire slide full magnification, and then convert this to other magnifications using convertRegionScale
. You would set sourceRegion['units']='base_pixels'
and then use getMagnificationForLevel
to determine the targetScale
argument value.
I'm having trouble obtaining the shape of the image level for each level. In OpenSlide, there is the parameter
slide.level_dimensions[level]
, but I haven't found anything similar in this library. How can I accomplish that?