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region encoder hotfix #52

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Merged
clemsgrs merged 2 commits into from
Jan 9, 2026
Merged

region encoder hotfix #52

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86458a9
fix import error
clemsgrs Jan 9, 2026
fcd93c5
use embedding key in RegionFeatureExtractor
clemsgrs Jan 9, 2026
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11 changes: 10 additions & 1 deletion slide2vec/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,15 @@ def log_progress(features_dir: Path, stop_event: threading.Event, log_interval:

def run_tiling(root_dir, config_file, output_dir):
print(f"Running tiling.py from {root_dir}...")

# add root_dir to PYTHONPATH so hs2p module can be found
env = os.environ.copy()
root_dir_abs = os.path.abspath(root_dir)
if "PYTHONPATH" in env:
env["PYTHONPATH"] = f"{root_dir_abs}:{env['PYTHONPATH']}"
else:
env["PYTHONPATH"] = root_dir_abs

cmd = [
sys.executable,
"hs2p/tiling.py",
Expand All @@ -61,7 +70,7 @@ def run_tiling(root_dir, config_file, output_dir):
"--skip-logging",
"wandb.enable=false", # disable wandb to avoid dupliacte logging
]
proc = subprocess.run(cmd, cwd=root_dir)
proc = subprocess.run(cmd, cwd=root_dir, env=env)
if proc.returncode != 0:
print("Slide tiling failed. Exiting.")
sys.exit(proc.returncode)
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4 changes: 2 additions & 2 deletions slide2vec/models/models.py
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Expand Up @@ -776,9 +776,9 @@ def forward(self, x):
# x = [B, num_tiles, 3, 224, 224]
B = x.size(0)
x = rearrange(x, "b p c w h -> (b p) c w h") # [B*num_tiles, 3, 224, 224]
output = self.tile_encoder(x) # [B*num_tiles, features_dim]
tile_embedding = self.tile_encoder(x)["embedding"] # [B*num_tiles, features_dim]
embedding = rearrange(
output, "(b p) f -> b p f", b=B
tile_embedding, "(b p) f -> b p f", b=B
) # [B, num_tiles, features_dim]
output = {"embedding": embedding}
return output
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