monai-weekly 1.5.dev2449__py3-none-any.whl → 1.5.dev2451__py3-none-any.whl

monai/__init__.py

@@ -136,4 +136,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "e604d1841fe60c0ffb6978ae4116535ca8d8f34f"
+__commit_id__ = "efff647a332f9520e7b7d7565893bd16ab26e041"

monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-12-08T02:32:52+0000",
+ "date": "2024-12-22T02:28:23+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "8cad248c8b374702245989507da1dd8430ef863f",
- "version": "1.5.dev2449"
+ "full-revisionid": "7c1c58cd10db72c01b5cdda1600cd68e262437cf",
+ "version": "1.5.dev2451"
 }
 '''  # END VERSION_JSON
 

monai/apps/utils.py

@@ -15,6 +15,7 @@ import hashlib
 import json
 import logging
 import os
+import re
 import shutil
 import sys
 import tarfile
@@ -30,7 +31,9 @@ from urllib.request import urlopen, urlretrieve
 from monai.config.type_definitions import PathLike
 from monai.utils import look_up_option, min_version, optional_import
 
+requests, has_requests = optional_import("requests")
 gdown, has_gdown = optional_import("gdown", "4.7.3")
+BeautifulSoup, has_bs4 = optional_import("bs4", name="BeautifulSoup")
 
 if TYPE_CHECKING:
     from tqdm import tqdm
@@ -298,6 +301,29 @@ def extractall(
     )
 
 
+def get_filename_from_url(data_url: str) -> str:
+    """
+    Get the filename from the URL link.
+    """
+    try:
+        response = requests.head(data_url, allow_redirects=True)
+        content_disposition = response.headers.get("Content-Disposition")
+        if content_disposition:
+            filename = re.findall('filename="?([^";]+)"?', content_disposition)
+            if filename:
+                return str(filename[0])
+        if "drive.google.com" in data_url:
+            response = requests.get(data_url)
+            if "text/html" in response.headers.get("Content-Type", ""):
+                soup = BeautifulSoup(response.text, "html.parser")
+                filename_div = soup.find("span", {"class": "uc-name-size"})
+                if filename_div:
+                    return str(filename_div.find("a").text)
+        return _basename(data_url)
+    except Exception as e:
+        raise Exception(f"Error processing URL: {e}") from e
+
+
 def download_and_extract(
     url: str,
     filepath: PathLike = "",
@@ -327,7 +353,18 @@ def download_and_extract(
             be False.
         progress: whether to display progress bar.
     """
+    url_filename_ext = "".join(Path(get_filename_from_url(url)).suffixes)
+    filepath_ext = "".join(Path(_basename(filepath)).suffixes)
+    if filepath not in ["", "."]:
+        if filepath_ext == "":
+            new_filepath = Path(filepath).with_suffix(url_filename_ext)
+            logger.warning(
+                f"filepath={filepath}, which missing file extension. Auto-appending extension to: {new_filepath}"
+            )
+            filepath = new_filepath
+    if filepath_ext and filepath_ext != url_filename_ext:
+        raise ValueError(f"File extension mismatch: expected extension {url_filename_ext}, but get {filepath_ext}")
     with tempfile.TemporaryDirectory() as tmp_dir:
-        filename = filepath or Path(tmp_dir, _basename(url)).resolve()
+        filename = filepath or Path(tmp_dir, get_filename_from_url(url)).resolve()
         download_url(url=url, filepath=filename, hash_val=hash_val, hash_type=hash_type, progress=progress)
         extractall(filepath=filename, output_dir=output_dir, file_type=file_type, has_base=has_base)

monai/engines/workflow.py

@@ -12,7 +12,7 @@
 from __future__ import annotations
 
 import warnings
-from collections.abc import Callable, Iterable, Sequence
+from collections.abc import Callable, Iterable, Sequence, Sized
 from typing import TYPE_CHECKING, Any
 
 import torch
@@ -121,24 +121,24 @@ class Workflow(Engine):
         to_kwargs: dict | None = None,
         amp_kwargs: dict | None = None,
     ) -> None:
-        if iteration_update is not None:
-            super().__init__(iteration_update)
-        else:
-            super().__init__(self._iteration)
+        super().__init__(self._iteration if iteration_update is None else iteration_update)
 
         if isinstance(data_loader, DataLoader):
-            sampler = data_loader.__dict__["sampler"]
+            sampler = getattr(data_loader, "sampler", None)
+
+            # set the epoch value for DistributedSampler objects when an epoch starts
             if isinstance(sampler, DistributedSampler):
 
                 @self.on(Events.EPOCH_STARTED)
                 def set_sampler_epoch(engine: Engine) -> None:
                     sampler.set_epoch(engine.state.epoch)
 
-            if epoch_length is None:
+        # if the epoch_length isn't given, attempt to get it from the length of the data loader
+        if epoch_length is None and isinstance(data_loader, Sized):
+            try:
                 epoch_length = len(data_loader)
-        else:
-            if epoch_length is None:
-                raise ValueError("If data_loader is not PyTorch DataLoader, must specify the epoch_length.")
+            except TypeError:  # raised when data_loader has an iterable dataset with no length, or is some other type
+                pass  # deliberately leave epoch_length as None
 
         # set all sharable data for the workflow based on Ignite engine.state
         self.state: Any = State(
@@ -147,7 +147,7 @@ class Workflow(Engine):
             iteration=0,
             epoch=0,
             max_epochs=max_epochs,
-            epoch_length=epoch_length,
+            epoch_length=epoch_length,  # None when the dataset is iterable and so has no length
             output=None,
             batch=None,
             metrics={},

{monai_weekly-1.5.dev2449.dist-info → monai_weekly-1.5.dev2451.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: monai-weekly
-Version: 1.5.dev2449
+Version: 1.5.dev2451
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium
@@ -46,10 +46,10 @@ Requires-Dist: itk>=5.2; extra == "all"
 Requires-Dist: tqdm>=4.47.0; extra == "all"
 Requires-Dist: lmdb; extra == "all"
 Requires-Dist: psutil; extra == "all"
-Requires-Dist: cucim-cu12; (python_version >= "3.9" and python_version <= "3.10") and extra == "all"
+Requires-Dist: cucim-cu12; (platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10") and extra == "all"
 Requires-Dist: openslide-python; extra == "all"
-Requires-Dist: tifffile; extra == "all"
-Requires-Dist: imagecodecs; extra == "all"
+Requires-Dist: tifffile; (platform_system == "Linux" or platform_system == "Darwin") and extra == "all"
+Requires-Dist: imagecodecs; (platform_system == "Linux" or platform_system == "Darwin") and extra == "all"
 Requires-Dist: pandas; extra == "all"
 Requires-Dist: einops; extra == "all"
 Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "all"
@@ -63,7 +63,7 @@ Requires-Dist: jsonschema; extra == "all"
 Requires-Dist: pynrrd; extra == "all"
 Requires-Dist: pydicom; extra == "all"
 Requires-Dist: h5py; extra == "all"
-Requires-Dist: nni; extra == "all"
+Requires-Dist: nni; (platform_system == "Linux" and "arm" not in platform_machine and "aarch" not in platform_machine) and extra == "all"
 Requires-Dist: optuna; extra == "all"
 Requires-Dist: onnx>=1.13.0; extra == "all"
 Requires-Dist: onnxruntime; python_version <= "3.10" and extra == "all"
@@ -101,13 +101,13 @@ Requires-Dist: lmdb; extra == "lmdb"
 Provides-Extra: psutil
 Requires-Dist: psutil; extra == "psutil"
 Provides-Extra: cucim
-Requires-Dist: cucim-cu12; extra == "cucim"
+Requires-Dist: cucim-cu12; (platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10") and extra == "cucim"
 Provides-Extra: openslide
 Requires-Dist: openslide-python; extra == "openslide"
 Provides-Extra: tifffile
-Requires-Dist: tifffile; extra == "tifffile"
+Requires-Dist: tifffile; (platform_system == "Linux" or platform_system == "Darwin") and extra == "tifffile"
 Provides-Extra: imagecodecs
-Requires-Dist: imagecodecs; extra == "imagecodecs"
+Requires-Dist: imagecodecs; (platform_system == "Linux" or platform_system == "Darwin") and extra == "imagecodecs"
 Provides-Extra: pandas
 Requires-Dist: pandas; extra == "pandas"
 Provides-Extra: einops
@@ -137,7 +137,7 @@ Requires-Dist: pydicom; extra == "pydicom"
 Provides-Extra: h5py
 Requires-Dist: h5py; extra == "h5py"
 Provides-Extra: nni
-Requires-Dist: nni; extra == "nni"
+Requires-Dist: nni; (platform_system == "Linux" and "arm" not in platform_machine and "aarch" not in platform_machine) and extra == "nni"
 Provides-Extra: optuna
 Requires-Dist: optuna; extra == "optuna"
 Provides-Extra: onnx

{monai_weekly-1.5.dev2449.dist-info → monai_weekly-1.5.dev2451.dist-info}/RECORD

@@ -1,5 +1,5 @@
-monai/__init__.py,sha256=8nDtqXXT8g-2RkTMzJScb7J2ivFmb37BrqgM3S_NJ1k,4095
-monai/_version.py,sha256=uJdYCwRIEg12C-k2c1DKHw0XzzOkPRe-G7r0glT9iYU,503
+monai/__init__.py,sha256=9uBqEYRgHOLxHMXL6KaeW64h3EEBWzVc8Q5_qNdvbHw,4095
+monai/_version.py,sha256=xt33zPGBBDISzFAylvD8rM8SeH-5WwgMQzCJR1hckIE,503
 monai/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 monai/_extensions/__init__.py,sha256=NEBPreRhQ8H9gVvgrLr_y52_TmqB96u_u4VQmeNT93I,642
 monai/_extensions/loader.py,sha256=7SiKw36q-nOzH8CRbBurFrz7GM40GCu7rc93Tm8XpnI,3643
@@ -10,7 +10,7 @@ monai/_extensions/gmm/gmm_cuda.cu,sha256=egWZBIpNYfOfxn0TKX82y-S2M6jg9NCzWwRcTLN
 monai/_extensions/gmm/gmm_cuda_linalg.cuh,sha256=Glqg2oAcUFUXg-DVfpROkiv-DdXvvVdM1nyiFm8qlHY,3520
 monai/apps/__init__.py,sha256=VDIc3HB_uFbqKL1TS-OeRvryEMDfzm22KJRzwpkXsGo,908
 monai/apps/datasets.py,sha256=msT58BoHlQFQpD4Tx-CThwAkkaUowoNZOgcH0THg0u0,35085
-monai/apps/utils.py,sha256=Gellkseuv3XKs-A6XcgbtqktQayv9NVIhX9tTQGM10I,14362
+monai/apps/utils.py,sha256=kJ200fyf_folGggBd2VK_CXjiDVMIAxaB6wxTj4NvBI,16099
 monai/apps/auto3dseg/__init__.py,sha256=DhUB2Ol0-iNAk1ZNmD1RkTODUOhdiibv8h9MgcLuF6s,1016
 monai/apps/auto3dseg/__main__.py,sha256=fCDhD8uhmJQKkKBxLO6hMJhEvZJRIsjTc1Ad3bYmNIY,1411
 monai/apps/auto3dseg/auto_runner.py,sha256=a4Ry93TkK0aTb68bwle8HoG4SzUbUf0IbDrY33jTReg,40106
@@ -151,7 +151,7 @@ monai/engines/__init__.py,sha256=oV0zH5n8qPdCCNZCqLqN4Z7iqADouDtZmtswWQoZWOk,109
 monai/engines/evaluator.py,sha256=d0V4Ko1mcVsr9PtOhhtJYy4SVtrXuKdZ9yWM9mCYpAA,26961
 monai/engines/trainer.py,sha256=CmCw0C20A1EUgmpBt_eGHp9ObIJO5shqF7bQGJVskc0,38448
 monai/engines/utils.py,sha256=YGaa1Gk2b3bBtodbToGaSOD-s9X7wMgfgESOozZCLrM,15632
-monai/engines/workflow.py,sha256=S4DCLBSndcaM6LDb6xS-gTL8xCs8fiVejb-8O-pLKeQ,15226
+monai/engines/workflow.py,sha256=FXZt8wN8m2U7wmXwoI0t1ILeieqsHtPwt5P8cMX71_A,15495
 monai/fl/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
 monai/fl/client/__init__.py,sha256=Wnkcf-Guhi-d29eAH0p51jz1Tn9WSVM4UUGbbb9SAqQ,725
 monai/fl/client/client_algo.py,sha256=vetQbSNmuvJRBEcu0AKM96gKYbkSXlu4HSriqK7wiiU,5098
@@ -420,8 +420,8 @@ monai/visualize/img2tensorboard.py,sha256=NnMcyfIFqX-jD7TBO3Rn02zt5uug79d_7pIIaV
 monai/visualize/occlusion_sensitivity.py,sha256=OQHEJLyIhB8zWqQsfKaX-1kvCjWFVYtLfS4dFC0nKFI,18160
 monai/visualize/utils.py,sha256=B-MhTVs7sQbIqYS3yPnpBwPw2K82rE2PBtGIfpwZtWM,9894
 monai/visualize/visualizer.py,sha256=qckyaMZCbezYUwE20k5yc-Pb7UozVavMDbrmyQwfYHY,1377
-monai_weekly-1.5.dev2449.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-monai_weekly-1.5.dev2449.dist-info/METADATA,sha256=pkXaiu1fplwCSKbFQn3lkiY_rbmynZAw6dJmE2RhjNk,11293
-monai_weekly-1.5.dev2449.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-monai_weekly-1.5.dev2449.dist-info/top_level.txt,sha256=UaNwRzLGORdus41Ip446s3bBfViLkdkDsXDo34J2P44,6
-monai_weekly-1.5.dev2449.dist-info/RECORD,,
+monai_weekly-1.5.dev2451.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+monai_weekly-1.5.dev2451.dist-info/METADATA,sha256=0Tg9NUHnzUVF_3-QgVzTfxt0yaQQ1X39LiDjn1THmws,11876
+monai_weekly-1.5.dev2451.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+monai_weekly-1.5.dev2451.dist-info/top_level.txt,sha256=UaNwRzLGORdus41Ip446s3bBfViLkdkDsXDo34J2P44,6
+monai_weekly-1.5.dev2451.dist-info/RECORD,,