monai-weekly 1.7.dev2636__tar.gz → 1.7.dev2637__tar.gz

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/MANIFEST.in

@@ -1,5 +1,6 @@
 include versioneer.py
 include monai/_version.py
+include monai/config/check_env.py
 
 include README.md
 include LICENSE

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.7.dev2636
+Version: 1.7.dev2637
 Summary: AI Toolkit for Healthcare Imaging
 Author-email: MONAI Consortium <monai.contact@gmail.com>
 License: Apache License 2.0

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/__init__.py

@@ -136,4 +136,4 @@ except Exception:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "d1306f6d1996cffeb9d10984dd1c056b7fe2ed1d"
+__commit_id__ = "3103fe7c3bed7952685ff05956fb85f112389a4f"

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2026-09-06T02:14:40+0000",
+ "date": "2026-09-13T02:14:44+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "917231cf0496c0a06cc1fe4c78822d570f8a2899",
- "version": "1.7.dev2636"
+ "full-revisionid": "d127996ee583969c8495840104c3c3326c0614ff",
+ "version": "1.7.dev2637"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/apps/auto3dseg/auto_runner.py

@@ -202,7 +202,7 @@ class AutoRunner:
 
         For the datalist file format, see the description under :py:func:`monai.data.load_decathlon_datalist`.
         Note that the AutoRunner will use the "validation" key in the datalist file if it exists, otherwise
-        it will do cross-validation, by default with five folds (this is hardcoded).
+        It will do cross-validation with the configured `num_fold` number of folds (default 5).
     """
 
     analyze_params: dict | None
@@ -398,8 +398,15 @@ class AutoRunner:
         Args:
             datalist_filename: path to the datalist file.
 
+        Returns:
+            Number of existing or generated folds, or 1 when using a validation list.
+
+        Raises:
+            ValueError: If training data is missing, fold IDs are not continuous from zero,
+                or the automatic fold count is outside [2, number of training items].
+
         Notes:
-            If the fold key is not provided, it auto generates 5 folds assignments in the training key list.
+            If the fold key is not provided, it generates the configured num_fold assignments (default 5).
             If validation key list is available, then it assumes a single fold validation.
         """
 
@@ -440,7 +447,12 @@ class AutoRunner:
             num_fold = 1
 
         else:
-            num_fold = 5
+            num_fold = int(self.data_src_cfg.get("num_fold", 5))
+            if not 2 <= num_fold <= len(datalist["training"]):
+                raise ValueError(
+                    "num_fold must be at least 2 and no greater than the number of training items "
+                    "when AutoRunner generates folds."
+                )
 
             warnings.warn(
                 f"Datalist has no folds specified {datalist_filename}..."

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/apps/detection/networks/retinanet_detector.py

@@ -41,7 +41,7 @@ from __future__ import annotations
 
 import warnings
 from collections.abc import Callable, Sequence
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 import torch
 from torch import Tensor, nn
@@ -59,10 +59,13 @@ from monai.inferers import SlidingWindowInferer
 from monai.networks.nets import resnet
 from monai.utils import BlendMode, PytorchPadMode, ensure_tuple_rep, optional_import
 
-BalancedPositiveNegativeSampler, _ = optional_import(
-    "torchvision.models.detection._utils", name="BalancedPositiveNegativeSampler"
-)
-Matcher, _ = optional_import("torchvision.models.detection._utils", name="Matcher")
+if TYPE_CHECKING:
+    from torchvision.models.detection._utils import BalancedPositiveNegativeSampler, Matcher
+else:
+    BalancedPositiveNegativeSampler, _ = optional_import(
+        "torchvision.models.detection._utils", name="BalancedPositiveNegativeSampler"
+    )
+    Matcher, _ = optional_import("torchvision.models.detection._utils", name="Matcher")
 
 
 class RetinaNetDetector(nn.Module):
@@ -769,10 +772,11 @@ class RetinaNetDetector(nn.Module):
             # BELOW_LOW_THRESHOLD = -1, BETWEEN_THRESHOLDS = -2
             if isinstance(self.proposal_matcher, Matcher):
                 # if torchvision matcher
+                matcher: Matcher = self.proposal_matcher
                 match_quality_matrix = self.box_overlap_metric(
                     targets_per_image[self.target_box_key].to(anchors_per_image.device), anchors_per_image
                 )
-                matched_idxs_per_image = self.proposal_matcher(match_quality_matrix)
+                matched_idxs_per_image = matcher(match_quality_matrix)
             elif isinstance(self.proposal_matcher, ATSSMatcher):
                 # if monai ATSS matcher
                 match_quality_matrix, matched_idxs_per_image = self.proposal_matcher(

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/apps/utils.py

@@ -378,7 +378,7 @@ def get_filename_from_url(data_url: str) -> str:
             filename = re.findall('filename="?([^";]+)"?', content_disposition)
             if filename:
                 return str(filename[0])
-        if "drive.google.com" in data_url:
+        if urlparse(data_url).netloc == "drive.google.com":
             response = requests.get(data_url)
             if "text/html" in response.headers.get("Content-Type", ""):
                 soup = BeautifulSoup(response.text, "html.parser")

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/config/__init__.py

@@ -14,7 +14,6 @@ from __future__ import annotations
 from .deviceconfig import (
     USE_COMPILED,
     USE_META_DICT,
-    IgniteInfo,
     get_config_values,
     get_gpu_info,
     get_optional_config_values,

monai_weekly-1.7.dev2637/monai/config/__main__.py

@@ -0,0 +1,15 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+if __name__ == "__main__":
+    import monai
+
+    monai.config.print_debug_info()  # type: ignore

monai_weekly-1.7.dev2637/monai/config/check_env.py

@@ -0,0 +1,184 @@
+#! /usr/bin/env python
+
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+Script for checking various elements of the runtime environment and printing a large amount of diagnostic information.
+
+This is meant to be used for debugging environments used with MONAI, but doesn't directly need MONAI itself. It will
+print information about the environment, including trying to get installed packages, test PyTorch with CUDA, and then
+have MONAI print its debugging information if no errors encountered. If MONAI is not installed this script should still
+work and produce useful information. Only standard libraries are needed in case a bare environment is being used.
+
+This can be run as a program with the following options to see all outputs:
+
+    python check_env.py --env --monai
+
+With no options at all this can be used to test that PyTorch is installed and can move a tensor to a device. This is
+useful when creating a fresh test environment and MONAI isn't present yet but it's good practice to valid PyTorch.
+Environment variables can be printed by using `--envars` with `--env`, however the output from this is not checked for
+secrets so users
+
+This can also be used remotely with only Python installed to get current environment diagnostic info:
+
+    curl https://raw.githubusercontent.com/Project-MONAI/MONAI/refs/heads/dev/monai/config/check_env.py | python
+"""
+
+from __future__ import annotations
+
+import argparse
+import getpass
+import multiprocessing
+import os
+import platform
+import shutil
+import subprocess
+import sys
+from functools import partial
+
+DESC = """
+Script for checking various elements of the runtime environment and printing a large amount of diagnostic information.
+This is used for debugging your environment by printing out various system statistics and diagnostic information. It
+checks PyTorch and MONAI are installed and functioning. A typical use case is with the `--env` and `--monai` options.
+"""
+
+USER = getpass.getuser()
+HOST = platform.node()
+efprint = partial(print, flush=True, file=sys.stderr)
+
+
+def fprint(*args, **kwargs):
+    """
+    Print with flushing, replacing the username and hostname values with placeholders for better anonymization.
+    """
+    kwargs["flush"] = True
+    content = " ".join(map(str, args))
+    content = content.replace(USER, "<user>").replace(HOST, "<host>")
+    print(content, **kwargs)
+
+
+def print_platform():
+    """
+    Print basic platform information.
+    """
+    fprint(platform.platform())
+    fprint("uname:", list(platform.uname()))
+    fprint("CPU:", platform.processor(), "Count:", multiprocessing.cpu_count())
+    fprint("Python:", sys.executable, platform.python_implementation(), platform.python_version())
+
+
+def print_environment_vars():
+    """
+    Print all environment variables other than a few known pointless ones.
+    """
+    fprint("Environment:")
+    for k, v in os.environ.items():
+        if k not in ("LS_COLORS", "PS1", "PS2"):
+            fprint(f"  {k}:", v)
+
+
+def print_environment():
+    """
+    Print the installed environment using `conda` or `pip`, fail if neither are present.
+    """
+    try:
+        cmd = ("conda", "env", "export") if shutil.which("conda") else ("pip", "list")
+
+        result = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
+        fprint(result.decode())
+        return True
+    except Exception as e:
+        efprint(f"Exception encountered getting environment with conda/pip: {e}")
+        return False
+
+
+def check_torch():
+    """
+    Check PyTorch is installed and a tensor can be created.
+    """
+    try:
+        import torch
+
+        t = torch.rand(2, 3) * 5
+        fprint("PyTorch:", torch.__version__, torch.__path__)
+        fprint("Test tensor:", t.flatten())
+        return True
+    except ImportError:
+        efprint("PyTorch not installed")
+        return False
+
+
+def check_torch_cuda():
+    """
+    Check CUDA capability in PyTorch by moving a tensor to each available device.
+    """
+    import torch
+
+    fprint("CUDA version:", torch.version.cuda)
+
+    try:
+        dcount = torch.cuda.device_count()
+        fprint("PyTorch GPU Count:", dcount)
+
+        for d in range(dcount):
+            fprint(f"  {torch.cuda.get_device_properties(d)}")
+            t = torch.rand(2, 3).to(torch.device(f"cuda:{d}")) * 5
+            fprint("Test tensor:", t.flatten())
+        return True
+    except Exception as e:
+        efprint(f"PyTorch encountered exception creating GPU tensor on device {d}: {e}")
+        return False
+
+
+def check_monai():
+    """
+    Check MONAI by importing it then printing its debug info.
+    """
+    try:
+        import monai
+
+        monai.config.print_debug_info()  # type: ignore
+        return True
+    except ImportError:
+        efprint("MONAI not installed")
+        return False
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(prog="check_env.py", description=DESC.strip())
+    parser.add_argument("--env", default=False, action="store_true", help="Print environment info")
+    parser.add_argument("--envvars", default=False, action="store_true", help="Include environment variables")
+    parser.add_argument("--monai", default=False, action="store_true", help="Print MONAI info")
+    args = parser.parse_args()
+
+    fprint("=" * 10, "Platform Info", "=" * 10)
+    print_platform()
+
+    if args.env:
+        fprint("=" * 10, "Checking Environment", "=" * 10)
+        if args.envvars:
+            print_environment_vars()
+        print_environment()
+
+    fprint("=" * 10, "Checking PyTorch", "=" * 10)
+
+    if not check_torch():
+        efprint("Exiting early, no valid PyTorch install found.")
+        sys.exit(1)
+
+    if not check_torch_cuda():
+        efprint("Exiting early, PyTorch encountered CUDA error.")
+        sys.exit(1)
+
+    if args.monai:
+        fprint("=" * 10, "Checking MONAI", "=" * 10)
+        check_monai()

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/config/deviceconfig.py

@@ -23,8 +23,6 @@ import numpy as np
 import torch
 
 import monai
-from monai.utils.deprecate_utils import deprecated
-from monai.utils.enums import IgniteInfo as _IgniteInfo
 from monai.utils.module import OptionalImportError, get_package_version, optional_import
 
 try:
@@ -47,9 +45,21 @@ __all__ = [
     "print_debug_info",
     "USE_COMPILED",
     "USE_META_DICT",
-    "IgniteInfo",
 ]
 
+USER = getpass.getuser()
+HOST = platform.node()
+
+
+def fprint(*args, **kwargs):
+    """
+    Print with flushing, replacing the username and hostname values with placeholders for better anonymization.
+    """
+    kwargs["flush"] = True
+    content = " ".join(map(str, args))
+    content = content.replace(USER, "<user>").replace(HOST, "<host>")
+    print(content, **kwargs)
+
 
 def get_config_values():
     """
@@ -100,17 +110,15 @@ def print_config(file=sys.stdout):
         file: `print()` text stream file. Defaults to `sys.stdout`.
     """
     for k, v in get_config_values().items():
-        print(f"{k} version: {v}", file=file, flush=True)
-    print(f"MONAI flags: HAS_EXT = {HAS_EXT}, USE_COMPILED = {USE_COMPILED}, USE_META_DICT = {USE_META_DICT}")
-    print(f"MONAI rev id: {monai.__revision_id__}")
-    username = getpass.getuser()
-    masked_file_path = re.sub(username, "<username>", monai.__file__)
-    print(f"MONAI __file__: {masked_file_path}", file=file, flush=True)
-    print("\nOptional dependencies:", file=file, flush=True)
+        fprint(f"{k} version: {v}", file=file)
+    fprint(f"MONAI flags: {HAS_EXT=}, {USE_COMPILED=}, {USE_META_DICT=}", file=file)
+    fprint(f"MONAI rev id: {monai.__revision_id__}", file=file)
+    fprint(f"MONAI __file__: {monai.__file__}", file=file)
+    fprint("\nOptional dependencies:", file=file)
     for k, v in get_optional_config_values().items():
-        print(f"{k} version: {v}", file=file, flush=True)
-    print("\nFor details about installing the optional dependencies, please visit:", file=file, flush=True)
-    print(
+        fprint(f"{k} version: {v}", file=file)
+    fprint("\nFor details about installing the optional dependencies, please visit:", file=file)
+    fprint(
         "    https://monai.readthedocs.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
         file=file,
         flush=True,
@@ -191,10 +199,10 @@ def print_system_info(file: TextIO = sys.stdout) -> None:
         file: `print()` text stream file. Defaults to `sys.stdout`.
     """
     if not has_psutil:
-        print("`psutil` required for `print_system_info`", file=file, flush=True)
+        fprint("`psutil` required for `print_system_info`", file=file)
     else:
         for k, v in get_system_info().items():
-            print(f"{k}: {v}", file=file, flush=True)
+            fprint(f"{k}: {v}", file=file)
 
 
 def get_gpu_info() -> OrderedDict:
@@ -239,7 +247,7 @@ def print_gpu_info(file: TextIO = sys.stdout) -> None:
         file: `print()` text stream file. Defaults to `sys.stdout`.
     """
     for k, v in get_gpu_info().items():
-        print(f"{k}: {v}", file=file, flush=True)
+        fprint(f"{k}: {v}", file=file)
 
 
 def print_debug_info(file: TextIO = sys.stdout) -> None:
@@ -249,26 +257,19 @@ def print_debug_info(file: TextIO = sys.stdout) -> None:
     Args:
         file: `print()` text stream file. Defaults to `sys.stdout`.
     """
-    print("================================", file=file, flush=True)
-    print("Printing MONAI config...", file=file, flush=True)
-    print("================================", file=file, flush=True)
+    fprint("================================", file=file)
+    fprint("Printing MONAI config...", file=file)
+    fprint("================================", file=file)
     print_config(file)
-    print("\n================================", file=file, flush=True)
-    print("Printing system config...")
-    print("================================", file=file, flush=True)
+    fprint("\n================================", file=file)
+    fprint("Printing system config...", file=file)
+    fprint("================================", file=file)
     print_system_info(file)
-    print("\n================================", file=file, flush=True)
-    print("Printing GPU config...")
-    print("================================", file=file, flush=True)
+    fprint("\n================================", file=file)
+    fprint("Printing GPU config...", file=file)
+    fprint("================================", file=file)
     print_gpu_info(file)
 
 
-@deprecated(since="1.4.0", removed="1.6.0", msg_suffix="Please use `monai.utils.enums.IgniteInfo` instead.")
-class IgniteInfo:
-    """Deprecated Import of IgniteInfo enum, which was moved to `monai.utils.enums.IgniteInfo`."""
-
-    OPT_IMPORT_VERSION = _IgniteInfo.OPT_IMPORT_VERSION
-
-
 if __name__ == "__main__":
     print_debug_info()

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/inferers/inferer.py

@@ -1773,7 +1773,7 @@ class ControlNetLatentDiffusionInferer(ControlNetDiffusionInferer):
         super().__init__(scheduler=scheduler)
         self.scale_factor = scale_factor
         if (ldm_latent_shape is None) ^ (autoencoder_latent_shape is None):
-            raise ValueError("If ldm_latent_shape is None, autoencoder_latent_shape must be None" "and vice versa.")
+            raise ValueError("If ldm_latent_shape is None, autoencoder_latent_shape must be None and vice versa.")
         self.ldm_latent_shape = ldm_latent_shape
         self.autoencoder_latent_shape = autoencoder_latent_shape
         if self.ldm_latent_shape is not None and self.autoencoder_latent_shape is not None:

{monai_weekly-1.7.dev2636 → monai_weekly-1.7.dev2637}/monai/losses/dice.py

@@ -22,7 +22,8 @@ from torch.nn.modules.loss import _Loss
 
 from monai.losses.focal_loss import FocalLoss
 from monai.losses.spatial_mask import MaskedLoss
-from monai.losses.utils import compute_tp_fp_fn
+from monai.losses.utils import compute_tp_fp_fn, mask_loss_inputs
+from monai.metrics.utils import create_ignore_mask
 from monai.networks import one_hot
 from monai.utils import DiceCEReduction, LossReduction, Weight, look_up_option
 
@@ -67,6 +68,7 @@ class DiceLoss(_Loss):
         batch: bool = False,
         weight: Sequence[float] | float | int | torch.Tensor | None = None,
         soft_label: bool = False,
+        ignore_index: int | None = None,
     ) -> None:
         """
         Args:
@@ -100,6 +102,10 @@ class DiceLoss(_Loss):
                 The value/values should be no less than 0. Defaults to None.
             soft_label: whether the target contains non-binary values (soft labels) or not.
                 If True a soft label formulation of the loss will be used.
+            ignore_index: single integer class index (or sentinel value) to ignore from the loss computation.
+                Voxels with this label are excluded from the loss, which is useful for padding, unlabeled regions,
+                or boundary artifacts. For federated or aggregated settings, ensure all clients use the same
+                ignore_index to keep loss values comparable.
 
         Raises:
             TypeError: When ``other_act`` is not an ``Optional[Callable]``.
@@ -122,6 +128,7 @@ class DiceLoss(_Loss):
         self.smooth_nr = float(smooth_nr)
         self.smooth_dr = float(smooth_dr)
         self.batch = batch
+        self.ignore_index = ignore_index
         weight = torch.as_tensor(weight) if weight is not None else None
         self.register_buffer("class_weight", weight)
         self.class_weight: None | torch.Tensor
@@ -163,10 +170,15 @@ class DiceLoss(_Loss):
         if self.other_act is not None:
             input = self.other_act(input)
 
+        original_target = target
+
         if self.to_onehot_y:
             if n_pred_ch == 1:
                 warnings.warn("single channel prediction, `to_onehot_y=True` ignored.", stacklevel=2)
             else:
+                if self.ignore_index is not None:
+                    if self.ignore_index < 0 or self.ignore_index >= n_pred_ch:
+                        target = torch.where(target == self.ignore_index, torch.zeros_like(target), target)
                 target = one_hot(target, num_classes=n_pred_ch)
 
         if not self.include_background:
@@ -177,9 +189,13 @@ class DiceLoss(_Loss):
                 target = target[:, 1:]
                 input = input[:, 1:]
 
+        mask = create_ignore_mask(original_target, self.ignore_index)
+
         if target.shape != input.shape:
             raise AssertionError(f"ground truth has different shape ({target.shape}) from input ({input.shape})")
 
+        input, target = mask_loss_inputs(input, target, self.ignore_index, mask=mask)
+
         # reducing only spatial dimensions (not batch nor channels)
         reduce_axis: list[int] = torch.arange(2, len(input.shape)).tolist()
         if self.batch: