sources/neuraloperator/examples/layers/plot_embeddings.py

"""
Grid Embeddings
===============

Grid embeddings encode spatial coordinates in neural operators, helping models understand geometric structure. This tutorial shows how to use:

- 2D and N-dimensional grid embeddings
- Custom coordinate systems
- Different embedding types for various domains

Grid embeddings are key for PDE solving, computer vision, and other spatially-structured problems. They add coordinate information and help neural operators learn spatial relationships.
"""

# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Import dependencies
# -------------------
# We import the necessary modules for working with grid embeddings

import random
import matplotlib.pyplot as plt
import torch

device = "cpu"

# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Understanding grid embeddings
# -----------------------------
# As we show in :ref:`small_darcy_vis`, we apply a 2D grid positional encoding to our data
# before passing it into the FNO. This embedding has been shown to improve model performance
# in a variety of applications by providing spatial context to the neural operator.
#
# Let's walk through its use. We start with a function that gives the coordinates of the
# bottom-left corners of each pixel in a grid:

from neuralop.layers.embeddings import regular_grid_2d

grid_2d = (
    torch.stack(regular_grid_2d(spatial_dims=(8, 8))).permute(1, 2, 0).view(-1, 2)
)  # reshape into (64, 2)

# Visualize the 2D grid coordinates
plt.scatter(grid_2d[:, 0], grid_2d[:, 1], color="orange", label="2D regular grid")
plt.legend()
plt.title("2D Grid Coordinates")
plt.xlabel("X coordinate")
plt.ylabel("Y coordinate")
plt.show()

# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Applying grid embeddings to data
# ---------------------------------
# In practice, we concatenate these two channels, representing the x- and y-coordinates
# of each pixel in an example, after the channels which encode physical variables
# in our PDE problems. This provides spatial context to the neural operator.

from neuralop.data.datasets import load_darcy_flow_small
from neuralop.layers.embeddings import GridEmbedding2D

# Load the Darcy-Flow dataset for demonstration
_, test_loaders, _ = load_darcy_flow_small(
    n_train=10,
    batch_size=1,
    test_resolutions=[16, 32],
    n_tests=[16, 16],
    test_batch_sizes=[2, 2],
    encode_output=False,
)

# Get a sample from the dataset
loader_16 = test_loaders[16]
example = next(iter(loader_16))
x = example["x"]
print(f"One batch of x is of shape: {x.shape}")

# Note: our Darcy dataset is generated on the unit square, but our grid
# embedding's boundaries are configurable.
grid_embedding = GridEmbedding2D(in_channels=1, grid_boundaries=[[0, 1], [0, 1]])
x = grid_embedding(x)
print(f"After embedding, x is of shape: {x.shape}")

# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Visualizing the embedded data
# -----------------------------
# We can visualize how the grid embedding adds coordinate information to our data.
# The embedding adds two channels: one for x-coordinates and one for y-coordinates.

# Grab the first element of the batch
x = x[0]
fig = plt.figure(figsize=(7, 7))

# Plot the original input data
ax = fig.add_subplot(2, 2, 1)
ax.imshow(x[0], cmap="gray")
ax.set_title("Input x")

# Plot the x-coordinate embedding
ax = fig.add_subplot(2, 2, 3)
ax.imshow(x[1])
ax.set_title("x-coordinate embedding")

# Plot the y-coordinate embedding
ax = fig.add_subplot(2, 2, 4)
ax.imshow(x[2])
ax.set_title("y-coordinate embedding")

fig.suptitle("Visualizing one input sample with positional embeddings", y=0.98)
plt.tight_layout()
fig.show()


# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Discretization invariance
# --------------------------
# Our embeddings are also designed with discretization-invariance in mind.
# Without any changes, we can apply the same embedding to higher-resolution data.
# This is crucial for neural operators that need to work at different resolutions.

loader_32 = test_loaders[32]
example = next(iter(loader_32))
x = example["x"]
print(f"One batch of x is of shape: {x.shape}")

# Apply the same grid embedding to higher-resolution data
x = grid_embedding(x)
print(f"After embedding, x is of shape: {x.shape}")

# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Visualizing higher-resolution embeddings
# ----------------------------------------
# We can see how the grid embedding scales to different resolutions.
# The coordinate information is automatically adjusted to the new grid size.

# Grab the first element of the batch
x = x[0]
fig = plt.figure(figsize=(7, 7))

# Plot the original input data
ax = fig.add_subplot(2, 2, 1)
ax.imshow(x[0], cmap="gray")
ax.set_title("Input x")

# Plot the x-coordinate embedding
ax = fig.add_subplot(2, 2, 3)
ax.imshow(x[1])
ax.set_title("x-coordinate embedding")

# Plot the y-coordinate embedding
ax = fig.add_subplot(2, 2, 4)
ax.imshow(x[2])
ax.set_title("y-coordinate embedding")

fig.suptitle("Visualizing one input sample with positional embeddings", y=0.98)
plt.tight_layout()
fig.show()

# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Understanding discretization invariance
# ---------------------------------------
# The grid embeddings automatically adapt to different resolutions:
# 1. The coordinate values are normalized to the same range regardless of resolution
# 2. The spatial relationships are preserved across different grid sizes
# 3. This allows neural operators to work seamlessly at different resolutions
# 4. The same model can be applied to data of varying spatial discretization

# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Working with 3D grid embeddings
# --------------------------------
# Let's also demonstrate how to embed a 3D tensor.
# This is useful for problems involving 3D spatial data, such as:
# - 3D fluid dynamics
# - Volumetric medical imaging
# - 3D material science problems

from neuralop.layers.embeddings import GridEmbeddingND

# Create a 3D tensor with one channel
cube_len = 5
x = torch.randn(1, 1, cube_len, cube_len, cube_len)
embedding_3d = GridEmbeddingND(in_channels=1, dim=3, grid_boundaries=[[0, 1]] * 3)

# Apply 3D grid embedding
x = embedding_3d(x)

# %%
# .. raw:: html
#
#    <div style="margin-top: 3em;"></div>
#
# Visualizing 3D grid embeddings
# ------------------------------
# We can visualize the 3D embeddings by showing the coordinate information
# in 3D space. Each point represents a spatial location with its coordinates.

# Grab only the appended positional embedding channels
x = x[0, 1:, ...].permute(1, 2, 3, 0).view(-1, 3)
fig, ax = plt.subplots(subplot_kw={"projection": "3d"})
plot = ax.scatter(x[:, 0], x[:, 1], x[:, 2], c=x[:, 2])
fig.colorbar(plot, ax=ax, shrink=0.6)
ax.set_title("3D positional encoding, color=Z value")
ax.set_xlabel("X")
ax.set_ylabel("Y")
ax.set_zlabel("Z")
plt.show()