monai-weekly 1.4.dev2436__tar.gz → 1.4.dev2438__tar.gz

{monai_weekly-1.4.dev2436/monai_weekly.egg-info → monai_weekly-1.4.dev2438}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: monai-weekly
-Version: 1.4.dev2436
+Version: 1.4.dev2438
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/__init__.py

@@ -135,4 +135,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "d02ba11d8069870d71316a616f047c499627c71c"
+__commit_id__ = "fa1c1af79ef5387434f2a76744f75b5aaca09f0b"

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-09-08T02:25:56+0000",
+ "date": "2024-09-22T02:28:25+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "0d9ab7da5ba0cbc2df3de3f7397c58ac1fe80598",
- "version": "1.4.dev2436"
+ "full-revisionid": "d85038e6acf92febeacfc53463a7e70e35d82670",
+ "version": "1.4.dev2438"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/bundle/scripts.py

@@ -255,6 +255,7 @@ def _download_from_ngc_private(
     else:
         raise ValueError("NGC API requires requests package. Please install it.")
 
+    os.makedirs(download_path, exist_ok=True)
     zip_path = download_path / f"{filename}_v{version}.zip"
     with open(zip_path, "wb") as f:
         f.write(response.content)

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/bundle/workflows.py

@@ -26,7 +26,7 @@ from monai.bundle.config_parser import ConfigParser
 from monai.bundle.properties import InferProperties, MetaProperties, TrainProperties
 from monai.bundle.utils import DEFAULT_EXP_MGMT_SETTINGS, EXPR_KEY, ID_REF_KEY, ID_SEP_KEY
 from monai.config import PathLike
-from monai.utils import BundleProperty, BundlePropertyConfig, deprecated_arg, deprecated_arg_default, ensure_tuple
+from monai.utils import BundleProperty, BundlePropertyConfig, deprecated_arg, ensure_tuple
 
 __all__ = ["BundleWorkflow", "ConfigWorkflow"]
 
@@ -43,7 +43,7 @@ class BundleWorkflow(ABC):
         workflow_type: specifies the workflow type: "train" or "training" for a training workflow,
             or "infer", "inference", "eval", "evaluation" for a inference workflow,
             other unsupported string will raise a ValueError.
-            default to `None` for common workflow.
+            default to `train` for train workflow.
         workflow: specifies the workflow type: "train" or "training" for a training workflow,
             or "infer", "inference", "eval", "evaluation" for a inference workflow,
             other unsupported string will raise a ValueError.
@@ -274,7 +274,6 @@ class ConfigWorkflow(BundleWorkflow):
         new_name="workflow_type",
         msg_suffix="please use `workflow_type` instead.",
     )
-    @deprecated_arg_default("workflow_type", None, "train", since="1.2", replaced="1.4")
     def __init__(
         self,
         config_file: str | Sequence[str],
@@ -284,7 +283,7 @@ class ConfigWorkflow(BundleWorkflow):
         run_id: str = "run",
         final_id: str = "finalize",
         tracking: str | dict | None = None,
-        workflow_type: str | None = None,
+        workflow_type: str | None = "train",
         workflow: str | None = None,
         properties_path: PathLike | None = None,
         **override: Any,

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/data/image_reader.py

@@ -1359,7 +1359,7 @@ class NrrdReader(ImageReader):
         x, y = direction.shape
         affine_diam = min(x, y) + 1
         affine: np.ndarray = np.eye(affine_diam)
-        affine[:x, :y] = direction
+        affine[:x, :y] = direction.T
         affine[: (affine_diam - 1), -1] = origin  # len origin is always affine_diam - 1
         return affine
 

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/handlers/__init__.py

@@ -20,7 +20,7 @@ from .decollate_batch import DecollateBatch
 from .earlystop_handler import EarlyStopHandler
 from .garbage_collector import GarbageCollector
 from .hausdorff_distance import HausdorffDistance
-from .ignite_metric import IgniteMetric, IgniteMetricHandler
+from .ignite_metric import IgniteMetricHandler
 from .logfile_handler import LogfileHandler
 from .lr_schedule_handler import LrScheduleHandler
 from .mean_dice import MeanDice

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/handlers/ignite_metric.py

@@ -20,7 +20,7 @@ from torch.nn.modules.loss import _Loss
 
 from monai.config import IgniteInfo
 from monai.metrics import CumulativeIterationMetric, LossMetric
-from monai.utils import MetricReduction, deprecated, min_version, optional_import
+from monai.utils import MetricReduction, min_version, optional_import
 
 idist, _ = optional_import("ignite", IgniteInfo.OPT_IMPORT_VERSION, min_version, "distributed")
 
@@ -153,25 +153,3 @@ class IgniteMetricHandler(Metric):
         self._name = name
         if self.save_details and not hasattr(engine.state, "metric_details"):
             engine.state.metric_details = {}  # type: ignore
-
-
-@deprecated(since="1.2", removed="1.4", msg_suffix="Use IgniteMetricHandler instead of IgniteMetric.")
-class IgniteMetric(IgniteMetricHandler):
-
-    def __init__(
-        self,
-        metric_fn: CumulativeIterationMetric | None = None,
-        loss_fn: _Loss | None = None,
-        output_transform: Callable = lambda x: x,
-        save_details: bool = True,
-        reduction: MetricReduction | str = MetricReduction.MEAN,
-        get_not_nans: bool = False,
-    ) -> None:
-        super().__init__(
-            metric_fn=metric_fn,
-            loss_fn=loss_fn,
-            output_transform=output_transform,
-            save_details=save_details,
-            reduction=reduction,
-            get_not_nans=get_not_nans,
-        )

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/losses/dice.py

@@ -24,7 +24,7 @@ from torch.nn.modules.loss import _Loss
 from monai.losses.focal_loss import FocalLoss
 from monai.losses.spatial_mask import MaskedLoss
 from monai.networks import one_hot
-from monai.utils import DiceCEReduction, LossReduction, Weight, deprecated_arg, look_up_option, pytorch_after
+from monai.utils import DiceCEReduction, LossReduction, Weight, look_up_option, pytorch_after
 
 
 class DiceLoss(_Loss):
@@ -646,9 +646,6 @@ class DiceCELoss(_Loss):
 
     """
 
-    @deprecated_arg(
-        "ce_weight", since="1.2", removed="1.4", new_name="weight", msg_suffix="please use `weight` instead."
-    )
     def __init__(
         self,
         include_background: bool = True,
@@ -662,7 +659,6 @@ class DiceCELoss(_Loss):
         smooth_nr: float = 1e-5,
         smooth_dr: float = 1e-5,
         batch: bool = False,
-        ce_weight: torch.Tensor | None = None,
         weight: torch.Tensor | None = None,
         lambda_dice: float = 1.0,
         lambda_ce: float = 1.0,
@@ -712,7 +708,6 @@ class DiceCELoss(_Loss):
         """
         super().__init__()
         reduction = look_up_option(reduction, DiceCEReduction).value
-        weight = ce_weight if ce_weight is not None else weight
         dice_weight: torch.Tensor | None
         if weight is not None and not include_background:
             dice_weight = weight[1:]
@@ -825,9 +820,6 @@ class DiceFocalLoss(_Loss):
 
     """
 
-    @deprecated_arg(
-        "focal_weight", since="1.2", removed="1.4", new_name="weight", msg_suffix="please use `weight` instead."
-    )
     def __init__(
         self,
         include_background: bool = True,
@@ -842,7 +834,6 @@ class DiceFocalLoss(_Loss):
         smooth_dr: float = 1e-5,
         batch: bool = False,
         gamma: float = 2.0,
-        focal_weight: Sequence[float] | float | int | torch.Tensor | None = None,
         weight: Sequence[float] | float | int | torch.Tensor | None = None,
         lambda_dice: float = 1.0,
         lambda_focal: float = 1.0,
@@ -885,7 +876,6 @@ class DiceFocalLoss(_Loss):
                 [0, 1]. Defaults to None.
         """
         super().__init__()
-        weight = focal_weight if focal_weight is not None else weight
         self.dice = DiceLoss(
             include_background=include_background,
             to_onehot_y=False,
@@ -994,9 +984,6 @@ class GeneralizedDiceFocalLoss(_Loss):
         ValueError: if either `lambda_gdl` or `lambda_focal` is less than 0.
     """
 
-    @deprecated_arg(
-        "focal_weight", since="1.2", removed="1.4", new_name="weight", msg_suffix="please use `weight` instead."
-    )
     def __init__(
         self,
         include_background: bool = True,
@@ -1010,7 +997,6 @@ class GeneralizedDiceFocalLoss(_Loss):
         smooth_dr: float = 1e-5,
         batch: bool = False,
         gamma: float = 2.0,
-        focal_weight: Sequence[float] | float | int | torch.Tensor | None = None,
         weight: Sequence[float] | float | int | torch.Tensor | None = None,
         lambda_gdl: float = 1.0,
         lambda_focal: float = 1.0,
@@ -1028,7 +1014,6 @@ class GeneralizedDiceFocalLoss(_Loss):
             smooth_dr=smooth_dr,
             batch=batch,
         )
-        weight = focal_weight if focal_weight is not None else weight
         self.focal = FocalLoss(
             include_background=include_background,
             to_onehot_y=to_onehot_y,

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/networks/blocks/patchembedding.py

@@ -21,7 +21,7 @@ from torch.nn import LayerNorm
 
 from monai.networks.blocks.pos_embed_utils import build_sincos_position_embedding
 from monai.networks.layers import Conv, trunc_normal_
-from monai.utils import deprecated_arg, ensure_tuple_rep, optional_import
+from monai.utils import ensure_tuple_rep, optional_import
 from monai.utils.module import look_up_option
 
 Rearrange, _ = optional_import("einops.layers.torch", name="Rearrange")
@@ -42,9 +42,6 @@ class PatchEmbeddingBlock(nn.Module):
 
     """
 
-    @deprecated_arg(
-        name="pos_embed", since="1.2", removed="1.4", new_name="proj_type", msg_suffix="please use `proj_type` instead."
-    )
     def __init__(
         self,
         in_channels: int,
@@ -52,7 +49,6 @@ class PatchEmbeddingBlock(nn.Module):
         patch_size: Sequence[int] | int,
         hidden_size: int,
         num_heads: int,
-        pos_embed: str = "conv",
         proj_type: str = "conv",
         pos_embed_type: str = "learnable",
         dropout_rate: float = 0.0,
@@ -69,8 +65,6 @@ class PatchEmbeddingBlock(nn.Module):
             pos_embed_type: position embedding layer type.
             dropout_rate: fraction of the input units to drop.
             spatial_dims: number of spatial dimensions.
-        .. deprecated:: 1.4
-            ``pos_embed`` is deprecated in favor of ``proj_type``.
         """
 
         super().__init__()

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/networks/nets/unetr.py

@@ -18,7 +18,7 @@ import torch.nn as nn
 from monai.networks.blocks.dynunet_block import UnetOutBlock
 from monai.networks.blocks.unetr_block import UnetrBasicBlock, UnetrPrUpBlock, UnetrUpBlock
 from monai.networks.nets.vit import ViT
-from monai.utils import deprecated_arg, ensure_tuple_rep
+from monai.utils import ensure_tuple_rep
 
 
 class UNETR(nn.Module):
@@ -27,9 +27,6 @@ class UNETR(nn.Module):
     UNETR: Transformers for 3D Medical Image Segmentation <https://arxiv.org/abs/2103.10504>"
     """
 
-    @deprecated_arg(
-        name="pos_embed", since="1.2", removed="1.4", new_name="proj_type", msg_suffix="please use `proj_type` instead."
-    )
     def __init__(
         self,
         in_channels: int,
@@ -39,7 +36,6 @@ class UNETR(nn.Module):
         hidden_size: int = 768,
         mlp_dim: int = 3072,
         num_heads: int = 12,
-        pos_embed: str = "conv",
         proj_type: str = "conv",
         norm_name: tuple | str = "instance",
         conv_block: bool = True,
@@ -67,9 +63,6 @@ class UNETR(nn.Module):
             qkv_bias: apply the bias term for the qkv linear layer in self attention block. Defaults to False.
             save_attn: to make accessible the attention in self attention block. Defaults to False.
 
-        .. deprecated:: 1.4
-            ``pos_embed`` is deprecated in favor of ``proj_type``.
-
         Examples::
 
             # for single channel input 4-channel output with image size of (96,96,96), feature size of 32 and batch norm

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/networks/nets/vit.py

@@ -18,7 +18,6 @@ import torch.nn as nn
 
 from monai.networks.blocks.patchembedding import PatchEmbeddingBlock
 from monai.networks.blocks.transformerblock import TransformerBlock
-from monai.utils import deprecated_arg
 
 __all__ = ["ViT"]
 
@@ -31,9 +30,6 @@ class ViT(nn.Module):
     ViT supports Torchscript but only works for Pytorch after 1.8.
     """
 
-    @deprecated_arg(
-        name="pos_embed", since="1.2", removed="1.4", new_name="proj_type", msg_suffix="please use `proj_type` instead."
-    )
     def __init__(
         self,
         in_channels: int,
@@ -43,7 +39,6 @@ class ViT(nn.Module):
         mlp_dim: int = 3072,
         num_layers: int = 12,
         num_heads: int = 12,
-        pos_embed: str = "conv",
         proj_type: str = "conv",
         pos_embed_type: str = "learnable",
         classification: bool = False,
@@ -75,9 +70,6 @@ class ViT(nn.Module):
             qkv_bias (bool, optional): apply bias to the qkv linear layer in self attention block. Defaults to False.
             save_attn (bool, optional): to make accessible the attention in self attention block. Defaults to False.
 
-        .. deprecated:: 1.4
-            ``pos_embed`` is deprecated in favor of ``proj_type``.
-
         Examples::
 
             # for single channel input with image size of (96,96,96), conv position embedding and segmentation backbone

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/networks/nets/vitautoenc.py

@@ -20,7 +20,7 @@ import torch.nn as nn
 from monai.networks.blocks.patchembedding import PatchEmbeddingBlock
 from monai.networks.blocks.transformerblock import TransformerBlock
 from monai.networks.layers import Conv
-from monai.utils import deprecated_arg, ensure_tuple_rep, is_sqrt
+from monai.utils import ensure_tuple_rep, is_sqrt
 
 __all__ = ["ViTAutoEnc"]
 
@@ -33,9 +33,6 @@ class ViTAutoEnc(nn.Module):
     Modified to also give same dimension outputs as the input size of the image
     """
 
-    @deprecated_arg(
-        name="pos_embed", since="1.2", removed="1.4", new_name="proj_type", msg_suffix="please use `proj_type` instead."
-    )
     def __init__(
         self,
         in_channels: int,
@@ -47,7 +44,6 @@ class ViTAutoEnc(nn.Module):
         mlp_dim: int = 3072,
         num_layers: int = 12,
         num_heads: int = 12,
-        pos_embed: str = "conv",
         proj_type: str = "conv",
         dropout_rate: float = 0.0,
         spatial_dims: int = 3,
@@ -71,9 +67,6 @@ class ViTAutoEnc(nn.Module):
             qkv_bias: apply bias to the qkv linear layer in self attention block. Defaults to False.
             save_attn: to make accessible the attention in self attention block. Defaults to False. Defaults to False.
 
-        .. deprecated:: 1.4
-            ``pos_embed`` is deprecated in favor of ``proj_type``.
-
         Examples::
 
             # for single channel input with image size of (96,96,96), conv position embedding and segmentation backbone

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/transforms/utils.py

@@ -582,7 +582,8 @@ def weighted_patch_samples(
     if not v[-1] or not isfinite(v[-1]) or v[-1] < 0:  # uniform sampling
         idx = r_state.randint(0, len(v), size=n_samples)
     else:
-        r, *_ = convert_to_dst_type(r_state.random(n_samples), v)
+        r_samples = r_state.random(n_samples)
+        r, *_ = convert_to_dst_type(r_samples, v, dtype=r_samples.dtype)
         idx = searchsorted(v, r * v[-1], right=True)  # type: ignore
     idx, *_ = convert_to_dst_type(idx, v, dtype=torch.int)  # type: ignore
     # compensate 'valid' mode

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/utils/enums.py

@@ -16,7 +16,6 @@ from enum import Enum
 from typing import TYPE_CHECKING
 
 from monai.config import IgniteInfo
-from monai.utils import deprecated
 from monai.utils.module import min_version, optional_import
 
 __all__ = [
@@ -56,7 +55,6 @@ __all__ = [
     "DataStatsKeys",
     "ImageStatsKeys",
     "LabelStatsKeys",
-    "AlgoEnsembleKeys",
     "HoVerNetMode",
     "HoVerNetBranch",
     "LazyAttr",
@@ -615,17 +613,6 @@ class LabelStatsKeys(StrEnum):
     LABEL_NCOMP = "ncomponents"
 
 
-@deprecated(since="1.2", removed="1.4", msg_suffix="please use `AlgoKeys` instead.")
-class AlgoEnsembleKeys(StrEnum):
-    """
-    Default keys for Mixed Ensemble
-    """
-
-    ID = "identifier"
-    ALGO = "infer_algo"
-    SCORE = "best_metric"
-
-
 class HoVerNetMode(StrEnum):
     """
     Modes for HoVerNet model:

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/monai/utils/misc.py

@@ -887,7 +887,7 @@ def run_cmd(cmd_list: list[str], **kwargs: Any) -> subprocess.CompletedProcess:
     if kwargs.pop("run_cmd_verbose", False):
         import monai
 
-        monai.apps.utils.get_logger("run_cmd").info(f"{cmd_list}")
+        monai.apps.utils.get_logger("run_cmd").info(f"{cmd_list}")  # type: ignore[attr-defined]
     try:
         return subprocess.run(cmd_list, **kwargs)
     except subprocess.CalledProcessError as e:

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438/monai_weekly.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: monai-weekly
-Version: 1.4.dev2436
+Version: 1.4.dev2438
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/tests/test_bundle_download.py

@@ -89,7 +89,7 @@ TEST_CASE_9 = [
 TEST_CASE_10 = [
     ["network.json", "test_output.pt", "test_input.pt", "large_files.yaml"],
     "test_bundle",
-    "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/test_bundle_v0.1.2.zip",
+    "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/test_bundle_v0.1.3.zip",
     {"model.pt": "27952767e2e154e3b0ee65defc5aed38", "model.ts": "97746870fe591f69ac09827175b00675"},
 ]
 

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/tests/test_nrrd_reader.py

@@ -40,8 +40,8 @@ TEST_CASE_8 = [
         "dimension": 4,
         "space": "left-posterior-superior",
         "sizes": [3, 4, 4, 1],
-        "space directions": [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]],
-        "space origin": [0.0, 0.0, 0.0],
+        "space directions": [[0.7, 0.0, 0.0], [0.0, 0.0, -0.8], [0.0, 0.9, 0.0]],
+        "space origin": [1.0, 5.0, 20.0],
     },
 ]
 
@@ -110,6 +110,10 @@ class TestNrrdReader(unittest.TestCase):
         np.testing.assert_allclose(image_array, test_image)
         self.assertIsInstance(image_header, dict)
         self.assertTupleEqual(tuple(image_header["spatial_shape"]), expected_shape)
+        np.testing.assert_allclose(
+            image_header["affine"],
+            np.array([[-0.7, 0.0, 0.0, -1.0], [0.0, 0.0, -0.9, -5.0], [0.0, -0.8, 0.0, 20.0], [0.0, 0.0, 0.0, 1.0]]),
+        )
 
     @parameterized.expand([TEST_CASE_8])
     def test_read_with_header_index_order_c(self, data_shape, filename, expected_shape, dtype, reference_header):

{monai_weekly-1.4.dev2436 → monai_weekly-1.4.dev2438}/tests/test_rand_weighted_crop.py

@@ -90,6 +90,21 @@ for p in TEST_NDARRAYS_ALL:
                 [[63, 37], [31, 43], [66, 20]],
             ]
         )
+        im = SEG1_2D
+        weight_map = np.zeros_like(im, dtype=np.int32)
+        weight_map[0, 30, 20] = 3
+        weight_map[0, 45, 44] = 1
+        weight_map[0, 60, 50] = 2
+        TESTS.append(
+            [
+                "int w 2d",
+                dict(spatial_size=(10, 12), num_samples=3),
+                p(im),
+                q(weight_map),
+                (1, 10, 12),
+                [[60, 50], [30, 20], [45, 44]],
+            ]
+        )
         im = SEG1_3D
         weight = np.zeros_like(im)
         weight[0, 5, 30, 17] = 1.1
@@ -149,6 +164,21 @@ for p in TEST_NDARRAYS_ALL:
                 [[32, 24, 40], [32, 24, 40], [32, 24, 40]],
             ]
         )
+        im = SEG1_3D
+        weight_map = np.zeros_like(im, dtype=np.int32)
+        weight_map[0, 6, 22, 19] = 4
+        weight_map[0, 8, 40, 31] = 2
+        weight_map[0, 13, 20, 24] = 3
+        TESTS.append(
+            [
+                "int w 3d",
+                dict(spatial_size=(8, 10, 12), num_samples=3),
+                p(im),
+                q(weight_map),
+                (1, 8, 10, 12),
+                [[13, 20, 24], [6, 22, 19], [8, 40, 31]],
+            ]
+        )
 
 
 class TestRandWeightedCrop(CropTest):