[DEGA-189] code for calculating spatial gradients and distributions with respect to regions

[huanlity]

1. move functions from notebooks to a separate .py file, including calculating distance, calculate gradient (bands), and plotting respective results.
2. to make the code more modular, reusable, and efficient, I organized the functions in the new .py file as a class.

The code can be called like this:

# Specify the polygon
roi_name = 'region_1'

# Initialize the class
distance_calculator = DistanceToPolygon(gdf_micron, gdf_join_micron, roi_name)

# Calculate distances
distance_calculator.calc_distance_to_polygon()

# Plot distances
distance_calculator.plot_distance_to_polygon()

# Calculate gene gradients
band_width = 200
distance_calculator.calc_gene_gradient_to_polygon(band_width=band_width, num_bands=5, gene_list=gene_list)

# Plot gene gradients
distance_calculator.plot_gene_gradient_to_polygon(gene_list=gene_list, markersize=1)

# Save bands to Parquet
distance_calculator.save_bands_to_parquet(f"{path_landscape_files}/gdf_{band_width}_um_bands_from_{roi_name}.parquet")

[cornhundred]

Hi @huanlity, I feel like I want to avoid making a class for this and we can instead use SpatialData (https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/tables.html) to store our state. Can you give that a try and let me know if you want to discuss?

Also, I want to use the Landscape visualization method to interactively visualize these regions and their associated gradients in addition to static plots. I think it is doable to add this to this pull request.