def test_get_embeddings():
backbone_arch = "resnet18"
model = TripletTrainerModel(pretrained=True, base_arch=backbone_arch)
data_path = fetch_example_dataset(dataset=ExampleData.TINY10)
dataset = ImageSingletDataset(
data_dir=data_path,
stage="train",
tile_type=TileType.ANCHOR,
transform=get_transforms(step="predict",
normalize_for_arch=backbone_arch),
)
# direct
dl_predict = DataLoader(dataset, batch_size=32)
batched_results = [model.forward(x_batch) for x_batch in dl_predict]
results = np.vstack([v.cpu().detach().numpy() for v in batched_results])
# via utily function
da_embeddings = get_embeddings(tile_dataset=dataset,
model=model,
prediction_batch_size=16)
Ntiles, Ndim = results.shape
assert int(da_embeddings.tile_id.count()) == Ntiles
assert int(da_embeddings.emb_dim.count()) == Ndim
def test_dendrogram_plot_triplets():
# use a model with default resnet weights to generate some embedding
# vectors to plot with
backbone_arch = "resnet18"
model = TripletTrainerModel(pretrained=True, base_arch=backbone_arch)
data_path = fetch_example_dataset(dataset=ExampleData.SMALL100)
tile_dataset = ImageTripletDataset(
data_dir=data_path,
stage="train",
transform=get_transforms(step="predict",
normalize_for_arch=backbone_arch),
)
da_embeddings = get_embeddings(tile_dataset=tile_dataset,
model=model,
prediction_batch_size=16)
for sampling_method in [
"random", "center_dist", "best_triplets", "worst_triplets"
]:
interpretation_plot.dendrogram(
da_embeddings=da_embeddings,
sampling_method=sampling_method,
tile_type="anchor",
)
def test_finetune_pretrained():
trainer = pl.Trainer(max_epochs=5, callbacks=[HeadFineTuner()])
arch = "resnet18"
model = TripletTrainerModel(pretrained=True, base_arch=arch)
data_path = fetch_example_dataset(dataset=ExampleData.TINY10)
datamodule = TripletTrainerDataModule(
data_dir=data_path, batch_size=2, normalize_for_arch=arch
)
trainer.fit(model=model, datamodule=datamodule)
def test_train_new_with_preloading():
trainer = pl.Trainer(max_epochs=5)
arch = "resnet18"
model = TripletTrainerModel(pretrained=False, base_arch=arch)
data_path = fetch_example_dataset(dataset=ExampleData.TINY10)
datamodule = TripletTrainerDataModule(
data_dir=data_path, batch_size=2, normalize_for_arch=arch, preload_data=True
)
trainer.fit(model=model, datamodule=datamodule)
def test_train_new_anti_aliased():
trainer = pl.Trainer(max_epochs=5, gpus=N_GPUS)
arch = "resnet18"
model = TripletTrainerModel(pretrained=False,
base_arch=arch,
anti_aliased_backbone=True)
data_path = fetch_example_dataset(dataset=ExampleData.TINY10)
datamodule = TripletTrainerDataModule(data_dir=data_path,
batch_size=2,
normalize_for_arch=arch)
trainer.fit(model=model, datamodule=datamodule)
def test_train_new_onecycle():
lr_monitor = LearningRateMonitor(logging_interval="step")
trainer = OneCycleTrainer(max_epochs=5,
callbacks=[lr_monitor],
gpus=N_GPUS)
arch = "resnet18"
model = TripletTrainerModel(pretrained=False, base_arch=arch)
data_path = fetch_example_dataset(dataset=ExampleData.TINY10)
datamodule = TripletTrainerDataModule(data_dir=data_path,
batch_size=2,
normalize_for_arch=arch)
trainer.fit(model=model, datamodule=datamodule)
def main(model_path, image_path):
model_path = Path(model_path)
model_name = model_path.parent.parent.name
model = TripletTrainerModel.load_from_checkpoint(model_path)
N_tile = (256, 256)
make_plot(model=model,
image_path=image_path,
model_name=model_name,
N_tile=N_tile)
scene_id = Path(image_path).name.split(".")[0]
output_img_filename = f"{model_name}.{scene_id}.PCA012_rgb.png"
plt.savefig(output_img_filename)
print(f"wrote image to `{output_img_filename}`")
def test_dendrogram_plot():
# use a model with default resnet weights to generate some embedding
# vectors to plot with
backbone_arch = "resnet18"
model = TripletTrainerModel(pretrained=True, base_arch=backbone_arch)
data_path = fetch_example_dataset(dataset=ExampleData.SMALL100)
tile_dataset = ImageSingletDataset(
data_dir=data_path,
stage="train",
tile_type=TileType.ANCHOR,
transform=get_transforms(step="predict",
normalize_for_arch=backbone_arch),
)
da_embeddings = get_embeddings(tile_dataset=tile_dataset,
model=model,
prediction_batch_size=16)
interpretation_plot.dendrogram(da_embeddings=da_embeddings)
def main(model_path, data_path):
if model_path.startswith("ex://"):
model_name = model_path[5:]
available_models = [m.name for m in list(PretrainedModel)]
if model_name not in available_models:
raise Exception(
f"pretrained model `{model_name}` not found."
f" available models: {', '.join(available_models)}"
)
model = load_pretrained_model(PretrainedModel[model_name])
else:
model = TripletTrainerModel.load_from_checkpoint(model_path)
if data_path.startswith("ex://"):
dset_name = data_path[5:]
available_dsets = [m.name for m in list(ExampleData)]
if model_name not in available_models:
raise Exception(
f"example dataset `{dset_name}` not found."
f" available dataset: {', '.join(available_dsets)}"
)
model = load_pretrained_model(PretrainedModel[model_name])
data_path = fetch_example_dataset(dataset=ExampleData[dset_name])
transforms = get_transforms(step="predict", normalize_for_arch=model.base_arch)
dset = ImageTripletDataset(data_dir=data_path, stage="train", transform=transforms)
embs_id = _make_hash(f"{model_path}__{data_path}")
fpath_embs = Path(f"embs-{embs_id}.nc")
if not fpath_embs.exists():
da_embs = get_embeddings(
tile_dataset=dset, model=model, prediction_batch_size=64
)
da_embs.to_netcdf(fpath_embs)
else:
da_embs = xr.open_dataarray(fpath_embs)
print(f"using saved embeddings from `{fpath_embs}`")
_save_embeddings(da_embs=da_embs, dset=dset)
def test_rectpred_sliding_window_inference():
# use a model with default resnet weights to generate some embedding
# vectors to plot with
backbone_arch = "resnet18"
model = TripletTrainerModel(pretrained=True, base_arch=backbone_arch)
# TODO: make this a property of the model
N_tile = (256, 256)
img = Image.open(RECTPRED_IMG_EXAMPLE_PATH)
step = (500, 200)
da_emb_rect = make_sliding_tile_model_predictions(img=img,
model=model,
step=step)
nx_img, ny_img = img.size
# number of tiles expected in each direction
nxt = (nx_img - N_tile[0] + step[0]) // step[0]
nyt = (ny_img - N_tile[1] + step[1]) // step[1]
assert da_emb_rect.emb_dim.count() == model.n_embedding_dims
assert da_emb_rect.i0.count() == nxt
assert da_emb_rect.j0.count() == nyt