Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ENH: add a --speedup option and tests #75

Merged
merged 15 commits into from
Jan 20, 2023
Merged

ENH: add a --speedup option and tests #75

Changes from 1 commit
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
515b2bb
add --speedup option to jit-compile model
kaczmarj Jan 20, 2023
3dca35b
fix typo in import alias
kaczmarj Jan 20, 2023
2a8d7f2
fix mypy complaint
kaczmarj Jan 20, 2023
7b51d6b
cache output of load_model
kaczmarj Jan 20, 2023
b7b2085
do not cache model because weights it not hashable
kaczmarj Jan 20, 2023
c4321d1
use eval mode for model in laod_model
kaczmarj Jan 20, 2023
fab20eb
rename _jit_compile to jit_compile
kaczmarj Jan 20, 2023
cc4ccf0
fix control flow in jit_compile
kaczmarj Jan 20, 2023
db1346f
add test_jit_compile
kaczmarj Jan 20, 2023
eebbf68
add tests on pytorch nightly
kaczmarj Jan 20, 2023
08a9be7
add ModelType type + use control flow for torch.compile
kaczmarj Jan 20, 2023
8afe7a5
cast model to Module if jit_compile
kaczmarj Jan 20, 2023
62520b5
using typing.cast instead of type.cast
kaczmarj Jan 20, 2023
645a62a
run regtests with and without --speedup
kaczmarj Jan 20, 2023
2410f4f
Merge remote-tracking branch 'refs/remotes/origin/enh/speedups' into …
kaczmarj Jan 20, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 8 additions & 4 deletions wsinfer/_modellib/run_inference.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@
from .models import Weights

PathType = typing.Union[str, Path]
ModelType = typing.Union[torch.jit.ScriptModule, torch.nn.Module, typing.Callable]


class WholeSlideImageDirectoryNotFound(FileNotFoundError):
Expand Down Expand Up @@ -165,7 +164,9 @@ def __getitem__(
return patch_im, torch.as_tensor([minx, miny, width, height])


def jit_compile(model: torch.nn.Module) -> ModelType:
def jit_compile(
model: torch.nn.Module,
) -> typing.Union[torch.jit.ScriptModule, torch.nn.Module, typing.Callable]:
"""JIT-compile a model for inference."""
noncompiled = model
w = "Warning: could not JIT compile the model. Using non-compiled model instead."
Expand Down Expand Up @@ -276,12 +277,15 @@ def run_inference(
model_output_dir.mkdir(exist_ok=True)

device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
model: ModelType = weights.load_model()
model = weights.load_model()
model.eval()
model.to(device)

if speedup:
model = jit_compile(model)
if typing.TYPE_CHECKING:
model = type.cast(torch.nn.Module, jit_compile(model))
kaczmarj marked this conversation as resolved.
Show resolved Hide resolved
else:
model = jit_compile(model)

# results_for_all_slides: typing.List[pd.DataFrame] = []
for i, (wsi_path, patch_path) in enumerate(zip(wsi_paths, patch_paths)):
Expand Down