dealing with moving ROIs/cells or ROIs from tracking

[pr4deepr]

Currently, napari-lattice works only with a single ROI and it assumes that the cell doesn't move much.
If cell wobbles a bit, we just draw a bigger ROI.
This is all done using the MIP image after image acquisition for Zeiss lattice.

We need to define how this is going to look like, i..e., scheme of the pydantic model if using this approach and best way to integrate it.

[multimeric]

Currently in my branch I define the ROIs as a list of shapes, each of which is defined as an array:

napari_lattice/core/lls_core/lattice_data.py

Line 158 in 17e10b6

roi_layer_list: ShapesData

To handle a movable ROI, we would need to define a new ROI type as a Pydantic model, which would at least contain the region as an array, and the timepoint it corresponds to:

class Roi(BaseModel):
    region: ShapesData
    time_point: int

Then the ROI list becomes a list of these new models:

class CropParams(BaseModel, arbitrary_types_allowed=True):
    roi_layer_list: List[Roi]

Finally, the logic to create CropParams, and to also to perform the cropping would have to change to accomodate this new structure and logic:

napari_lattice/core/lls_core/lattice_data.py

Lines 452 to 468 in 17e10b6

	yield ProcessedVolume(
	data = crop_volume_deskew(
	original_volume=data,
	deconvolution=self.deconv_enabled,
	get_deskew_and_decon=False,
	debug=False,
	roi_shape=roi,
	linear_interpolation=True,
	voxel_size_x=self.dx,
	voxel_size_y=self.dy,
	voxel_size_z=self.dy,
	angle_in_degrees=self.angle,
	deskewed_volume=self.deskewed_volume,
	z_start=self.crop.z_start,
	z_end=self.crop.z_end,
	**deconv_args
	),