Edge Cases when binding to nearest level

[FloCF]

Just two tiny super nitpicky things you might consider.

I’d slightly change this function:

TRIDENT/trident/wsi_objects/WSIPatcher.py

Lines 343 to 348 in a6305ac

	def _prepare(self) -> None:
	level, _ = self.wsi.get_best_level_and_custom_downsample(self.downsample, tolerance=0.1)
	level_downsample = int(self.wsi.level_downsamples[level])
	patch_size_level = round(self.patch_size_src / level_downsample)
	overlap_level = round(self.overlap_src / level_downsample)
	return level, patch_size_level, overlap_level

Into something like:

  def _prepare(self) -> None:
      level, level_downsample = self.wsi.get_best_level_and_custom_downsample(self.downsample, tolerance=0.1)
      patch_size_level = round(self.patch_size_target *  level_downsample)
      # overlap_level = round(self.overlap * level_downsample) # I guess this is never used
      return level, patch_size_level #, overlap_level

Why?
In cases where you bind to the nearest level, I think the patch size at that level should exactly match the desired output patch size.
Otherwise, the level patch size might be slightly smaller than the actual patch size, leading to minor resizing artefacts.
Situations when this is triggered are what I mean:

TRIDENT/trident/wsi_objects/WSI.py

Lines 607 to 609 in a6305ac

	for level, level_downsample in enumerate(level_downsamples):
	if abs(level_downsample - downsample) <= tolerance:
	return level, 1.0 # Exact match, no custom downsampling needed

Speaking of binding — I’d probably only “push up” cases that are just below the upper-level downsample rate, for efficiency.
If the requested downsample is already above that level, I’d stay exact, since there’s no real speed gain from binding.

So maybe change this:

TRIDENT/trident/wsi_objects/WSI.py

Lines 607 to 609 in a6305ac

	for level, level_downsample in enumerate(level_downsamples):
	if abs(level_downsample - downsample) <= tolerance:
	return level, 1.0 # Exact match, no custom downsampling needed

Into something like this:

# If the actual downsample is just below a specific level-downsample within tolerance, push to that level for efficiency
for level, level_downsample in enumerate(level_downsamples):
  if 0 <= (level_downsample - downsample) <= tolerance:
      return level, 1.0  # Exact match, no custom downsampling needed

Let me know if you’d like me to open a PR with these changes.
I’m currently building a preprocessing pipeline myself and have been heavily inspired by your work here!

[FloCF]

Thinking about it a bit more carefully: if you only make the above changes, your patch_size_src and overlap_src will no longer match, since your new downsample after binding is slightly different.

You could adapt the _prepare function to update self.downsample, and then change the order here:

TRIDENT/trident/wsi_objects/WSIPatcher.py

Lines 139 to 143 in a6305ac

	self.downsample = self.dst_pixel_size / self.src_pixel_size
	self.patch_size_src = round(patch_size * self.downsample)
	self.overlap_src = round(overlap * self.downsample)
	self.level, self.patch_size_level, self.overlap_level = self._prepare()

like this

    self.downsample = self.dst_pixel_size / self.src_pixel_size
    self.level, self.patch_size_level, self.overlap_level = self._prepare()
    self.patch_size_src = round(patch_size * self.downsample)
    self.overlap_src = round(overlap * self.downsample)

Not sure if all this is worth the trouble 🤷.
Let me know if you want me to propose a small PR.