slide2vec 1.2.1__tar.gz → 1.2.2__tar.gz

{slide2vec-1.2.1/slide2vec.egg-info → slide2vec-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 1.2.1
+Version: 1.2.2
 Summary: Embedding of whole slide images with Foundation Models
 Home-page: https://github.com/clemsgrs/slide2vec
 Author: Clément Grisi

{slide2vec-1.2.1 → slide2vec-1.2.2}/pyproject.toml

@@ -23,7 +23,7 @@ warn_unused_configs = true
 no_implicit_reexport = true
 
 [tool.bumpver]
-current_version = "1.2.1"
+current_version = "1.2.2"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit = false       # We do version bumping in CI, not as a commit
 tag = false          # Git tag already exists — we don't auto-tag

{slide2vec-1.2.1 → slide2vec-1.2.2}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = slide2vec
-version = 1.2.1
+version = 1.2.2
 description = Embedding of whole slide images with Foundation Models
 author = Clément Grisi
 platforms = unix, linux, osx, cygwin, win32

slide2vec-1.2.2/slide2vec/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.2.2"

{slide2vec-1.2.1 → slide2vec-1.2.2}/slide2vec/aggregate.py

@@ -170,9 +170,9 @@ def main(args):
     ]
     print("=+=" * 10)
     print(f"Total number of slides with tile-level features: {slides_with_tile_features}/{total_slides}")
-    print(f"Failed slide-level feature aggregation: {len(failed_feature_aggregation)}")
+    print(f"Failed slide-level feature aggregation: {len(failed_feature_aggregation)}/{total_slides}")
     print(
-        f"Completed slide-level feature aggregation: {total_slides - len(failed_feature_aggregation)}"
+        f"Completed slide-level feature aggregation: {total_slides - len(failed_feature_aggregation)}/{total_slides}"
     )
     print("=+=" * 10)
 

{slide2vec-1.2.1 → slide2vec-1.2.2}/slide2vec/distributed/__init__.py

@@ -1,8 +1,8 @@
+import datetime
 import os
 import random
 import re
 import socket
-import datetime
 from typing import Dict, List
 
 import torch
@@ -278,7 +278,11 @@ def enable(
             _check_env_variable(key, value)
         os.environ[key] = value
 
-    dist.init_process_group(backend="nccl", timeout=datetime.timedelta(days=14))
+    dist.init_process_group(
+        backend="nccl",
+        timeout=datetime.timedelta(days=14),
+        device_id=torch.device(f"cuda:{torch_env.local_rank}")
+    )
     dist.barrier()
 
     # Finalize setup

{slide2vec-1.2.1 → slide2vec-1.2.2}/slide2vec/embed.py

@@ -275,7 +275,7 @@ def main(args):
             print(f"Total number of slides with {unit}s: {slides_with_tiles}/{total_slides}")
             print(f"Failed {unit}-level feature extraction: {len(failed_feature_extraction)}/{slides_with_tiles}")
             print(
-                f"Completed {unit}-level feature extraction: {slides_with_tiles - len(failed_feature_extraction)}"
+                f"Completed {unit}-level feature extraction: {slides_with_tiles - len(failed_feature_extraction)}/{slides_with_tiles}"
             )
             print("=+=" * 10)
 

{slide2vec-1.2.1 → slide2vec-1.2.2}/slide2vec/main.py

@@ -1,16 +1,16 @@
+import argparse
 import os
-import sys
-import time
-import wandb
-import socket
 import signal
-import argparse
-import threading
+import socket
 import subprocess
-
+import sys
+import threading
+import time
 from pathlib import Path
 
-from slide2vec.utils.config import setup, hf_login
+import wandb
+
+from slide2vec.utils.config import hf_login, setup
 
 
 def get_args_parser(add_help: bool = True):
@@ -41,10 +41,22 @@ def run_tiling(config_file, run_id):
         "--config-file",
         config_file,
     ]
-    result = subprocess.run(cmd)
-    if result.returncode != 0:
+    proc = subprocess.Popen(
+        cmd,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        text=True,
+        bufsize=1,
+        universal_newlines=True
+    )
+    # forward output in real-time
+    for line in proc.stdout:
+        print(line.rstrip())
+        sys.stdout.flush()
+    proc.wait()
+    if proc.returncode != 0:
         print("Slide tiling failed. Exiting.")
-        sys.exit(result.returncode)
+        sys.exit(proc.returncode)
 
 
 def run_feature_extraction(config_file, run_id):
@@ -69,10 +81,18 @@ def run_feature_extraction(config_file, run_id):
     proc = subprocess.Popen(
         cmd,
         preexec_fn=os.setsid,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
         text=True,
+        bufsize=1,
+        universal_newlines=True
     )
     try:
-        proc.communicate()
+        # forward output in real-time
+        for line in proc.stdout:
+            print(line.rstrip())
+            sys.stdout.flush()
+        proc.wait()
     except KeyboardInterrupt:
         print("Received CTRL+C, terminating embed.py process group...")
         os.killpg(os.getpgid(proc.pid), signal.SIGTERM)
@@ -98,10 +118,18 @@ def run_feature_aggregation(config_file, run_id):
     proc = subprocess.Popen(
         cmd,
         preexec_fn=os.setsid,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
         text=True,
+        bufsize=1,
+        universal_newlines=True
     )
     try:
-        proc.communicate()
+        # forward output in real-time
+        for line in proc.stdout:
+            print(line.rstrip())
+            sys.stdout.flush()
+        proc.wait()
     except KeyboardInterrupt:
         print("Received CTRL+C, terminating embed.py process group...")
         os.killpg(os.getpgid(proc.pid), signal.SIGTERM)
@@ -153,6 +181,7 @@ def main(args):
 
 if __name__ == "__main__":
     import warnings
+
     import torchvision
     torchvision.disable_beta_transforms_warning()
 

{slide2vec-1.2.1 → slide2vec-1.2.2}/slide2vec/models/models.py

@@ -161,7 +161,7 @@ class DINOViT(FeatureExtractor):
         nn.modules.utils.consume_prefix_in_state_dict_if_present(
             state_dict, prefix="backbone."
         )
-        state_dict, msg = update_state_dict(self.encoder.state_dict(), state_dict)
+        state_dict, msg = update_state_dict(model_dict=self.encoder.state_dict(), state_dict=state_dict)
         if distributed.is_main_process():
             print(msg)
         self.encoder.load_state_dict(state_dict, strict=False)
@@ -242,7 +242,7 @@ class CustomViT(FeatureExtractor):
         nn.modules.utils.consume_prefix_in_state_dict_if_present(
             state_dict, prefix="backbone."
         )
-        state_dict, msg = update_state_dict(self.encoder.state_dict(), state_dict)
+        state_dict, msg = update_state_dict(model_dict=self.encoder.state_dict(), state_dict=state_dict)
         if distributed.is_main_process():
             print(msg)
         self.encoder.load_state_dict(state_dict, strict=False)

{slide2vec-1.2.1 → slide2vec-1.2.2}/slide2vec/utils/config.py

@@ -56,7 +56,7 @@ def setup(config_file):
 
     output_dir = Path(cfg.output_dir, run_id)
     if distributed.is_main_process():
-        output_dir.mkdir(exist_ok=True, parents=True)
+        output_dir.mkdir(exist_ok=cfg.resume, parents=True)
     cfg.output_dir = str(output_dir)
 
     fix_random_seeds(0)

{slide2vec-1.2.1 → slide2vec-1.2.2}/slide2vec/utils/utils.py

@@ -126,7 +126,11 @@ def load_csv(cfg):
     return wsi_paths, mask_paths
 
 
-def update_state_dict(model_dict, state_dict):
+def update_state_dict(
+    *,
+    model_dict: dict,
+    state_dict: dict,
+):
     """
     Matches weights between `model_dict` and `state_dict`, accounting for:
     - Key mismatches (missing in model_dict)
@@ -166,13 +170,13 @@ def update_state_dict(model_dict, state_dict):
                     break
         if not matched_key:
             # key not found in state_dict
-            updated_state_dict[model_key] = model_val  # Keep original weights
+            updated_state_dict[model_key] = model_val  # keep original weights
             missing_keys += 1
             missing_keys_list.append(model_key)
-    # Log summary
-    msg = (
-        f"{success}/{len(model_dict)} weight(s) loaded successfully\n"
-        f"{shape_mismatch} weight(s) not loaded due to mismatching shapes: {shape_mismatch_list}\n"
-        f"{missing_keys} key(s) from checkpoint not found in model: {missing_keys_list}"
-    )
-    return updated_state_dict, msg
+    # log summary
+    msg = f"{success}/{len(model_dict)} weight(s) loaded successfully"
+    if shape_mismatch > 0:
+        msg += f"\n{shape_mismatch} weight(s) not loaded due to mismatching shapes: {shape_mismatch_list}"
+    if missing_keys > 0:
+        msg += f"\n{missing_keys} key(s) from checkpoint not found in model: {missing_keys_list}"
+    return updated_state_dict, msg

{slide2vec-1.2.1 → slide2vec-1.2.2}/slide2vec/wsi/wsi.py

@@ -306,7 +306,7 @@ class WholeSlideImage(object):
         # resize the mask to the size of the slide at seg_spacing
         mask = cv2.resize(
             mask.astype(np.uint8),
-            (int(height / scale), int(width / scale)),
+            (int(round(height / scale, 0)), int(round(width / scale, 0))),
             interpolation=cv2.INTER_NEAREST,
         )
 

{slide2vec-1.2.1 → slide2vec-1.2.2/slide2vec.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 1.2.1
+Version: 1.2.2
 Summary: Embedding of whole slide images with Foundation Models
 Home-page: https://github.com/clemsgrs/slide2vec
 Author: Clément Grisi

slide2vec-1.2.1/slide2vec/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.1"