import torch
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import sys
from gpsa import VariationalGPSA, matern12_kernel, rbf_kernel
from gpsa.plotting import callback_twod
sys.path.append("../../data")
from simulated.generate_twod_data import generate_twod_data
import matplotlib.animation as animation
import matplotlib.image as mpimg
import os
from os.path import join as pjoin
import anndata
import matplotlib
from matplotlib.lines import Line2D
font = {"size": 20}
matplotlib.rc("font", **font)
matplotlib.rcParams["text.usetex"] = True
device = "cuda" if torch.cuda.is_available() else "cpu"
LATEX_FONTSIZE = 35
n_spatial_dims = 2
n_views = 2
m_G = 50
m_X_per_view = 50
N_EPOCHS = 2000
PRINT_EVERY = 100
ONE_SAMPLE_FIXED = True
def two_d_gpsa(
n_outputs,
n_epochs,
n_latent_gps,
warp_kernel_variance=0.1,
noise_variance=0.0,
plot_intermediate=True,
fixed_view_idx=None,
):
X, Y, n_samples_list, view_idx = generate_twod_data(
n_views,
n_outputs,
grid_size=10,
n_latent_gps=n_latent_gps["expression"],
kernel_lengthscale=5.0,
kernel_variance=warp_kernel_variance,
noise_variance=noise_variance,
fixed_view_idx=0 if ONE_SAMPLE_FIXED else None,
)
n_samples_per_view = X.shape[0] // n_views
plt.figure(figsize=(7, 5))
markers = ["o", "X"]
for vv in range(n_views):
plt.scatter(
X[view_idx[vv]][:, 0],
X[view_idx[vv]][:, 1],
c=Y[view_idx[vv]][:, 0],
s=400,
marker=markers[vv],
label="View {}".format(vv + 1),
edgecolor="black",
linewidth=2,
)
plt.xlabel("X1")
plt.ylabel("X2")
plt.legend(loc="center left", bbox_to_anchor=(1, 0.5))
plt.tight_layout()
plt.savefig("./../../examples/synthetic_data_example.png")
plt.close()
## Save as anndata object
data_obj = anndata.AnnData(Y)
data_obj.obsm["spatial"] = X
batch_id = np.concatenate([[xx] * n_samples_list[xx] for xx in range(n_views)])
data_obj.obs["batch"] = batch_id
data_obj.write("../../examples/synthetic_data.h5ad")
x = torch.from_numpy(X).float().clone()
y = torch.from_numpy(Y).float().clone()
data_dict = {
"expression": {
"spatial_coords": x,
"outputs": y,
"n_samples_list": n_samples_list,
}
}
model = VariationalGPSA(
data_dict,
n_spatial_dims=n_spatial_dims,
m_X_per_view=m_X_per_view,
m_G=m_G,
data_init=True,
minmax_init=False,
grid_init=False,
n_latent_gps=n_latent_gps,
mean_function="identity_fixed",
kernel_func_warp=rbf_kernel,
kernel_func_data=rbf_kernel,
fixed_view_idx=fixed_view_idx,
).to(device)
view_idx, Ns, _, _ = model.create_view_idx_dict(data_dict)
optimizer = torch.optim.Adam(model.parameters(), lr=1e-2)
def train(model, loss_fn, optimizer):
model.train()
# Forward pass
G_means, G_samples, F_latent_samples, F_samples = model.forward(
{"expression": x}, view_idx=view_idx, Ns=Ns, S=5
)
# Compute loss
loss = loss_fn(data_dict, F_samples)
# Compute gradients and take optimizer step
optimizer.zero_grad()
loss.backward()
optimizer.step()
return loss.item()
# Set up figure.
fig = plt.figure(figsize=(12.14, 5), facecolor="white", constrained_layout=True)
data_expression_ax = fig.add_subplot(121, frameon=False)
latent_expression_ax = fig.add_subplot(122, frameon=False)
plt.show(block=False)
loss_trace = []
error_trace = []
n_frames = 0
for t in range(n_epochs):
loss = train(model, model.loss_fn, optimizer)
loss_trace.append(loss)
if plot_intermediate and t % PRINT_EVERY == 0:
print("Iter: {0:<10} LL {1:1.3e}".format(t, -loss))
G_means, G_samples, F_latent_samples, F_samples = model.forward(
{"expression": x}, view_idx=view_idx, Ns=Ns
)
callback_twod(
model,
X,
Y,
data_expression_ax=data_expression_ax,
latent_expression_ax=latent_expression_ax,
X_aligned=G_means,
s=600,
)
legend_elements = [
Line2D(
[0],
[0],
marker="o",
color="w",
label="Slice 1",
markerfacecolor="black",
markersize=20,
),
Line2D(
[0],
[0],
marker="X",
color="w",
label="Slice 2",
markerfacecolor="black",
markersize=20,
),
]
# Create the figure
plt.legend(
handles=legend_elements, loc="center left", bbox_to_anchor=(1, 0.5)
)
plt.tight_layout()
# plt.draw()
plt.savefig("./tmp/tmp{}".format(n_frames))
n_frames += 1
# plt.pause(1 / 60.0)
G_means, G_samples, F_latent_samples, F_samples = model.forward(
{"expression": x}, view_idx=view_idx, Ns=Ns
)
print("Done!")
plt.close()
fig = plt.figure()
ims = []
for ii in range(n_frames):
fname = "./tmp/tmp{}.png".format(ii)
img = mpimg.imread(fname)
im = plt.imshow(img)
ax = plt.gca()
ax.set_yticks([])
ax.set_xticks([])
ims.append([im])
os.remove(fname)
writervideo = animation.FFMpegWriter(fps=5)
ani = animation.ArtistAnimation(fig, ims, interval=50, blit=True, repeat_delay=500)
if ONE_SAMPLE_FIXED:
save_name = "alignment_animation_template.gif"
else:
save_name = "alignment_animation.gif"
ani.save(
pjoin("out", save_name),
writer=writervideo,
dpi=1000,
)
plt.close()
if __name__ == "__main__":
n_outputs = 30
two_d_gpsa(
n_epochs=N_EPOCHS,
n_outputs=n_outputs,
warp_kernel_variance=0.5,
noise_variance=0.001,
n_latent_gps={"expression": 5},
fixed_view_idx=0,
)
import ipdb
ipdb.set_trace()