Axis order might have been inconsistent

[qin-yu]

There appears to be a discrepancy in how the resolution axes are handled. The naming convention and the effect on the resolution axes seem to differ in various parts of the code.

1. The code snippet here reads and parses the ZYX resolution from a TIFF file into VoxelSize. This part of the code appears to work correctly. However, the naming convention used is __XY, which might be misleading because the effect seems to be __YX.
   

   plant-seg/plantseg/io/tiff.py

   Lines 141 to 144 in 53d12bd

   	if layout == "ZXY":
   	assert stack.ndim == 3, "Stack dimensions must be in ZXY order"
   	z, y, x = stack.shape
   	stack = stack.reshape(1, z, 1, y, x, 1)

2. The function here correctly reads and parses the resolution, and ZYX is passed into VoxelSize.
   

   plant-seg/plantseg/io/tiff.py

   Lines 32 to 41 in 53d12bd

   	# parse X, Y resolution
   	y = _xy_voxel_size(tags, "YResolution")
   	x = _xy_voxel_size(tags, "XResolution")
   	# return voxel size
   	if x is None or y is None:
   	gui_logger.warning("Error parsing imagej tiff meta.")
   	return VoxelSize()
   	return VoxelSize(voxels_size=(z, y, x), unit=voxel_size_unit)

3. The code snippet here outputs ZXY resolution from VoxelSize, which aligns with the intended behavior but does not match the actual effect observed.
   

   plant-seg/plantseg/io/utils.py

   Lines 76 to 95 in 53d12bd

   	@property
   	def z(self) -> float:
   	"""Safe access to the voxel size in the z direction. return 1.0 if the voxel size is not defined."""
   	if self.voxels_size is None:
   	return 1.0
   	return self.voxels_size[0]
   	@property
   	def x(self) -> float:
   	"""Safe access to the voxel size in the x direction. return 1.0 if the voxel size is not defined."""
   	if self.voxels_size is None:
   	return 1.0
   	return self.voxels_size[1]
   	@property
   	def y(self) -> float:
   	"""Safe access to the voxel size in the y direction. return 1.0 if the voxel size is not defined."""
   	if self.voxels_size is None:
   	return 1.0
   	return self.voxels_size[2]

[qin-yu]

I didn't mark this as a bug because I'm not 100% sure.

[qin-yu]

I just realised the ImageLayout always uses XY. But just confirmed that TIFF and HDF5 both have __YX/__HW and both pytorch3dunet and PlantSeg might have been using __YX effectively.

[lorenzocerrone]

The XY or YX is a harmless convention (unless you do measurements or have an XY anisotropy). Most tools agree on XY, but plantseg and pyotrch3dunet don't. But I would be in favor of moving to YX everywhere.