monai-weekly 1.4.dev2430__py3-none-any.whl → 1.4.dev2434__py3-none-any.whl

monai/networks/utils.py

@@ -822,7 +822,7 @@ def _onnx_trt_compile(
     output_names = [] if not output_names else output_names
 
     # set up the TensorRT builder
-    torch_tensorrt.set_device(device)
+    torch.cuda.set_device(device)
     logger = trt.Logger(trt.Logger.WARNING)
     builder = trt.Builder(logger)
     network = builder.create_network(1 << int(trt.NetworkDefinitionCreationFlag.EXPLICIT_BATCH))
@@ -931,7 +931,7 @@ def convert_to_trt(
         warnings.warn(f"The dynamic batch range sequence should have 3 elements, but got {dynamic_batchsize} elements.")
 
     device = device if device else 0
-    target_device = torch.device(f"cuda:{device}") if device else torch.device("cuda:0")
+    target_device = torch.device(f"cuda:{device}")
     convert_precision = torch.float32 if precision == "fp32" else torch.half
     inputs = [torch.rand(ensure_tuple(input_shape)).to(target_device)]
 
@@ -986,7 +986,7 @@ def convert_to_trt(
                     ir_model,
                     inputs=input_placeholder,
                     enabled_precisions=convert_precision,
-                    device=target_device,
+                    device=torch_tensorrt.Device(f"cuda:{device}"),
                     ir="torchscript",
                     **kwargs,
                 )

monai/transforms/__init__.py

@@ -688,6 +688,7 @@ from .utils import (
     weighted_patch_samples,
     zero_margins,
 )
+from .utils_morphological_ops import dilate, erode
 from .utils_pytorch_numpy_unification import (
     allclose,
     any_np_pt,

monai/transforms/io/array.py

@@ -86,7 +86,7 @@ def switch_endianness(data, new="<"):
         if new not in ("<", ">"):
             raise NotImplementedError(f"Not implemented option new={new}.")
         if current_ != new:
-            data = data.byteswap().newbyteorder(new)
+            data = data.byteswap().view(data.dtype.newbyteorder(new))
     elif isinstance(data, tuple):
         data = tuple(switch_endianness(x, new) for x in data)
     elif isinstance(data, list):

monai/transforms/post/array.py

@@ -211,7 +211,8 @@ class AsDiscrete(Transform):
             raise ValueError("`to_onehot=True/False` is deprecated, please use `to_onehot=num_classes` instead.")
         img = convert_to_tensor(img, track_meta=get_track_meta())
         img_t, *_ = convert_data_type(img, torch.Tensor)
-        if argmax or self.argmax:
+        argmax = self.argmax if argmax is None else argmax
+        if argmax:
             img_t = torch.argmax(img_t, dim=self.kwargs.get("dim", 0), keepdim=self.kwargs.get("keepdim", True))
 
         to_onehot = self.to_onehot if to_onehot is None else to_onehot

monai/transforms/spatial/functional.py

@@ -373,7 +373,7 @@ def rotate(img, angle, output_shape, mode, padding_mode, align_corners, dtype, l
     if output_shape is None:
         corners = np.asarray(np.meshgrid(*[(0, dim) for dim in im_shape], indexing="ij")).reshape((len(im_shape), -1))
         corners = transform[:-1, :-1] @ corners  # type: ignore
-        output_shape = np.asarray(corners.ptp(axis=1) + 0.5, dtype=int)
+        output_shape = np.asarray(np.ptp(corners, axis=1) + 0.5, dtype=int)
     else:
         output_shape = np.asarray(output_shape, dtype=int)
     shift = create_translate(input_ndim, ((np.array(im_shape) - 1) / 2).tolist())

monai/transforms/transform.py

@@ -203,8 +203,8 @@ class Randomizable(ThreadUnsafe, RandomizableTrait):
 
         """
         if seed is not None:
-            _seed = id(seed) if not isinstance(seed, (int, np.integer)) else seed
-            _seed = _seed % MAX_SEED
+            _seed = np.int64(id(seed) if not isinstance(seed, (int, np.integer)) else seed)
+            _seed = _seed % MAX_SEED  # need to account for Numpy2.0 which doesn't silently convert to int64
             self.R = np.random.RandomState(_seed)
             return self
 

monai/transforms/utils.py

@@ -22,6 +22,7 @@ from typing import Any
 
 import numpy as np
 import torch
+from torch import Tensor
 
 import monai
 from monai.config import DtypeLike, IndexSelection
@@ -30,6 +31,7 @@ from monai.networks.layers import GaussianFilter
 from monai.networks.utils import meshgrid_ij
 from monai.transforms.compose import Compose
 from monai.transforms.transform import MapTransform, Transform, apply_transform
+from monai.transforms.utils_morphological_ops import erode
 from monai.transforms.utils_pytorch_numpy_unification import (
     any_np_pt,
     ascontiguousarray,
@@ -65,6 +67,8 @@ from monai.utils import (
     min_version,
     optional_import,
     pytorch_after,
+    unsqueeze_left,
+    unsqueeze_right,
 )
 from monai.utils.enums import TransformBackends
 from monai.utils.type_conversion import (
@@ -103,6 +107,8 @@ __all__ = [
     "generate_spatial_bounding_box",
     "get_extreme_points",
     "get_largest_connected_component_mask",
+    "get_largest_connected_component_mask_point",
+    "convert_points_to_disc",
     "remove_small_objects",
     "img_bounds",
     "in_bounds",
@@ -1172,6 +1178,183 @@ def get_largest_connected_component_mask(
     return convert_to_dst_type(out, dst=img, dtype=out.dtype)[0]
 
 
+def get_largest_connected_component_mask_point(
+    img_pos: NdarrayTensor,
+    img_neg: NdarrayTensor,
+    point_coords: NdarrayTensor,
+    point_labels: NdarrayTensor,
+    pos_val: Sequence[int] = (1, 3),
+    neg_val: Sequence[int] = (0, 2),
+    margins: int = 3,
+) -> NdarrayTensor:
+    """
+    Gets the connected component of img_pos and img_neg that include the positive points and
+    negative points separately. The function is used for combining automatic results with interactive
+    results in VISTA3D.
+
+    Args:
+        img_pos: bool type tensor, shape [B, 1, H, W, D], where B means the foreground masks from a single 3D image.
+        img_neg: same format as img_pos but corresponds to negative points.
+        pos_val: positive point label values.
+        neg_val: negative point label values.
+        point_coords: the coordinates of each point, shape [B, N, 3], where N means the number of points.
+        point_labels: the label of each point, shape [B, N].
+    """
+
+    cucim_skimage, has_cucim = optional_import("cucim.skimage")
+
+    use_cp = has_cp and has_cucim and isinstance(img_pos, torch.Tensor) and img_pos.device != torch.device("cpu")
+    if use_cp:
+        img_pos_ = convert_to_cupy(img_pos.short())  # type: ignore
+        img_neg_ = convert_to_cupy(img_neg.short())  # type: ignore
+        label = cucim_skimage.measure.label
+        lib = cp
+    else:
+        if not has_measure:
+            raise RuntimeError("skimage.measure required.")
+        img_pos_, *_ = convert_data_type(img_pos, np.ndarray)
+        img_neg_, *_ = convert_data_type(img_neg, np.ndarray)
+        # for skimage.measure.label, the input must be bool type
+        if img_pos_.dtype != bool or img_neg_.dtype != bool:
+            raise ValueError("img_pos and img_neg must be bool type.")
+        label = measure.label
+        lib = np
+
+    features_pos, _ = label(img_pos_, connectivity=3, return_num=True)
+    features_neg, _ = label(img_neg_, connectivity=3, return_num=True)
+
+    outs = np.zeros_like(img_pos_)
+    for bs in range(point_coords.shape[0]):
+        for i, p in enumerate(point_coords[bs]):
+            if point_labels[bs, i] in pos_val:
+                features = features_pos
+            elif point_labels[bs, i] in neg_val:
+                features = features_neg
+            else:
+                # if -1 padding point, skip
+                continue
+            for margin in range(margins):
+                if isinstance(p, np.ndarray):
+                    x, y, z = np.round(p).astype(int).tolist()
+                else:
+                    x, y, z = p.float().round().int().tolist()
+                l, r = max(x - margin, 0), min(x + margin + 1, features.shape[-3])
+                t, d = max(y - margin, 0), min(y + margin + 1, features.shape[-2])
+                f, b = max(z - margin, 0), min(z + margin + 1, features.shape[-1])
+                if (features[bs, 0, l:r, t:d, f:b] > 0).any():
+                    index = features[bs, 0, l:r, t:d, f:b].max()
+                    outs[[bs]] += lib.isin(features[[bs]], index)
+                    break
+    outs[outs > 1] = 1
+    return convert_to_dst_type(outs, dst=img_pos, dtype=outs.dtype)[0]
+
+
+def convert_points_to_disc(
+    image_size: Sequence[int], point: Tensor, point_label: Tensor, radius: int = 2, disc: bool = False
+):
+    """
+    Convert a 3D point coordinates into image mask. The returned mask has the same spatial
+    size as `image_size` while the batch dimension is the same as 'point' batch dimension.
+    The point is converted to a mask ball with radius defined by `radius`. The output
+    contains two channels each for negative (first channel) and positive points.
+
+    Args:
+        image_size: The output size of the converted mask. It should be a 3D tuple.
+        point: [B, N, 3], 3D point coordinates.
+        point_label: [B, N], 0 or 2 means negative points, 1 or 3 means postive points.
+        radius: disc ball radius size.
+        disc: If true, use regular disc, other use gaussian.
+    """
+    masks = torch.zeros([point.shape[0], 2, image_size[0], image_size[1], image_size[2]], device=point.device)
+    _array = [
+        torch.arange(start=0, end=image_size[i], step=1, dtype=torch.float32, device=point.device) for i in range(3)
+    ]
+    coord_rows, coord_cols, coord_z = torch.meshgrid(_array[2], _array[1], _array[0])
+    # [1, 3, h, w, d] -> [b, 2, 3, h, w, d]
+    coords = unsqueeze_left(torch.stack((coord_rows, coord_cols, coord_z), dim=0), 6)
+    coords = coords.repeat(point.shape[0], 2, 1, 1, 1, 1)
+    for b, n in np.ndindex(*point.shape[:2]):
+        point_bn = unsqueeze_right(point[b, n], 4)
+        if point_label[b, n] > -1:
+            channel = 0 if (point_label[b, n] == 0 or point_label[b, n] == 2) else 1
+            pow_diff = torch.pow(coords[b, channel] - point_bn, 2)
+            if disc:
+                masks[b, channel] += pow_diff.sum(0) < radius**2
+            else:
+                masks[b, channel] += torch.exp(-pow_diff.sum(0) / (2 * radius**2))
+    return masks
+
+
+def sample_points_from_label(
+    labels: Tensor,
+    label_set: Sequence[int],
+    max_ppoint: int = 1,
+    max_npoint: int = 0,
+    device: torch.device | str | None = "cpu",
+    use_center: bool = False,
+):
+    """Sample points from labels.
+
+    Args:
+        labels: [1, 1, H, W, D]
+        label_set: local index, must match values in labels.
+        max_ppoint: maximum positive point samples.
+        max_npoint: maximum negative point samples.
+        device: returned tensor device.
+        use_center: whether to sample points from center.
+
+    Returns:
+        point: point coordinates of [B, N, 3]. B equals to the length of label_set.
+        point_label: [B, N], always 0 for negative, 1 for positive.
+    """
+    if not labels.shape[0] == 1:
+        raise ValueError("labels must have batch size 1.")
+
+    if device is None:
+        device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+
+    labels = labels[0, 0]
+    unique_labels = labels.unique().cpu().numpy().tolist()
+    _point = []
+    _point_label = []
+    for id in label_set:
+        if id in unique_labels:
+            plabels = labels == int(id)
+            nlabels = ~plabels
+            _plabels = get_largest_connected_component_mask(erode(plabels.unsqueeze(0).unsqueeze(0))[0, 0])
+            plabelpoints = torch.nonzero(_plabels).to(device)
+            if len(plabelpoints) == 0:
+                plabelpoints = torch.nonzero(plabels).to(device)
+            nlabelpoints = torch.nonzero(nlabels).to(device)
+            num_p = min(len(plabelpoints), max_ppoint)
+            num_n = min(len(nlabelpoints), max_npoint)
+            pad = max_ppoint + max_npoint - num_p - num_n
+            if use_center:
+                pmean = plabelpoints.float().mean(0)
+                pdis = ((plabelpoints - pmean) ** 2).sum(-1)
+                _, sorted_indices_tensor = torch.sort(pdis)
+                sorted_indices = sorted_indices_tensor.cpu().tolist()
+            else:
+                sorted_indices = list(range(len(plabelpoints)))
+                random.shuffle(sorted_indices)
+            _point.append(
+                torch.stack(
+                    [plabelpoints[sorted_indices[i]] for i in range(num_p)]
+                    + random.choices(nlabelpoints, k=num_n)
+                    + [torch.tensor([0, 0, 0], device=device)] * pad
+                )
+            )
+            _point_label.append(torch.tensor([1] * num_p + [0] * num_n + [-1] * pad).to(device))
+        else:
+            # pad the background labels
+            _point.append(torch.zeros(max_ppoint + max_npoint, 3).to(device))
+            _point_label.append(torch.zeros(max_ppoint + max_npoint).to(device) - 1)
+    point = torch.stack(_point)
+    point_label = torch.stack(_point_label)
+
+    return point, point_label
+
+
 def remove_small_objects(
     img: NdarrayTensor,
     min_size: int = 64,

monai/{apps/generation/maisi/utils/morphological_ops.py → transforms/utils_morphological_ops.py}

@@ -20,6 +20,8 @@ from torch import Tensor
 from monai.config import NdarrayOrTensor
 from monai.utils import convert_data_type, convert_to_dst_type, ensure_tuple_rep
 
+__all__ = ["erode", "dilate"]
+
 
 def erode(mask: NdarrayOrTensor, filter_size: int | Sequence[int] = 3, pad_value: float = 1.0) -> NdarrayOrTensor:
     """

monai/transforms/utils_pytorch_numpy_unification.py

@@ -480,7 +480,7 @@ def max(x: NdarrayTensor, dim: int | tuple | None = None, **kwargs) -> NdarrayTe
         else:
             ret = torch.max(x, int(dim), **kwargs)  # type: ignore
 
-    return ret
+    return ret[0] if isinstance(ret, tuple) else ret
 
 
 def mean(x: NdarrayTensor, dim: int | tuple | None = None, **kwargs) -> NdarrayTensor:
@@ -546,7 +546,7 @@ def min(x: NdarrayTensor, dim: int | tuple | None = None, **kwargs) -> NdarrayTe
         else:
             ret = torch.min(x, int(dim), **kwargs)  # type: ignore
 
-    return ret
+    return ret[0] if isinstance(ret, tuple) else ret
 
 
 def std(x: NdarrayTensor, dim: int | tuple | None = None, unbiased: bool = False) -> NdarrayTensor:

monai/utils/module.py

@@ -13,7 +13,6 @@ from __future__ import annotations
 
 import enum
 import functools
-import importlib.util
 import os
 import pdb
 import re
@@ -209,10 +208,11 @@ def load_submodules(
     ):
         if (is_pkg or load_all) and name not in sys.modules and match(exclude_pattern, name) is None:
             try:
+                mod = import_module(name)
                 mod_spec = importer.find_spec(name)  # type: ignore
                 if mod_spec and mod_spec.loader:
-                    mod = importlib.util.module_from_spec(mod_spec)
-                    mod_spec.loader.exec_module(mod)
+                    loader = mod_spec.loader
+                    loader.exec_module(mod)
                     submodules.append(mod)
             except OptionalImportError:
                 pass  # could not import the optional deps., they are ignored
@@ -564,7 +564,7 @@ def version_leq(lhs: str, rhs: str) -> bool:
     """
 
     lhs, rhs = str(lhs), str(rhs)
-    pkging, has_ver = optional_import("pkg_resources", name="packaging")
+    pkging, has_ver = optional_import("packaging.Version")
     if has_ver:
         try:
             return cast(bool, pkging.version.Version(lhs) <= pkging.version.Version(rhs))
@@ -591,7 +591,8 @@ def version_geq(lhs: str, rhs: str) -> bool:
 
     """
     lhs, rhs = str(lhs), str(rhs)
-    pkging, has_ver = optional_import("pkg_resources", name="packaging")
+    pkging, has_ver = optional_import("packaging.Version")
+
     if has_ver:
         try:
             return cast(bool, pkging.version.Version(lhs) >= pkging.version.Version(rhs))
@@ -629,7 +630,7 @@ def pytorch_after(major: int, minor: int, patch: int = 0, current_ver_string: st
         if current_ver_string is None:
             _env_var = os.environ.get("PYTORCH_VER", "")
             current_ver_string = _env_var if _env_var else torch.__version__
-        ver, has_ver = optional_import("pkg_resources", name="parse_version")
+        ver, has_ver = optional_import("packaging.version", name="parse")
         if has_ver:
             return ver(".".join((f"{major}", f"{minor}", f"{patch}"))) <= ver(f"{current_ver_string}")  # type: ignore
         parts = f"{current_ver_string}".split("+", 1)[0].split(".", 3)

{monai_weekly-1.4.dev2430.dist-info → monai_weekly-1.4.dev2434.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: monai-weekly
-Version: 1.4.dev2430
+Version: 1.4.dev2434
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium
@@ -29,125 +29,127 @@ Classifier: Typing :: Typed
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown; charset=UTF-8
 License-File: LICENSE
-Requires-Dist: torch >=1.9
-Requires-Dist: numpy >=1.20
+Requires-Dist: torch>=1.9
+Requires-Dist: numpy<2.0,>=1.24
 Provides-Extra: all
-Requires-Dist: nibabel ; extra == 'all'
-Requires-Dist: ninja ; extra == 'all'
-Requires-Dist: scikit-image >=0.14.2 ; extra == 'all'
-Requires-Dist: pillow ; extra == 'all'
-Requires-Dist: tensorboard ; extra == 'all'
-Requires-Dist: gdown >=4.7.3 ; extra == 'all'
-Requires-Dist: pytorch-ignite ==0.4.11 ; extra == 'all'
-Requires-Dist: torchvision ; extra == 'all'
-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: openslide-python ; extra == 'all'
-Requires-Dist: tifffile ; extra == 'all'
-Requires-Dist: imagecodecs ; extra == 'all'
-Requires-Dist: pandas ; extra == 'all'
-Requires-Dist: einops ; extra == 'all'
-Requires-Dist: mlflow >=2.12.2 ; extra == 'all'
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-Requires-Dist: tensorboardX ; extra == 'all'
-Requires-Dist: pyyaml ; extra == 'all'
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-Requires-Dist: h5py ; extra == 'all'
-Requires-Dist: nni ; extra == 'all'
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-Requires-Dist: nvidia-ml-py ; extra == 'all'
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-Requires-Dist: scipy >=1.12.0 ; (python_version >= "3.9") and extra == 'all'
-Requires-Dist: cucim-cu12 ; (python_version >= "3.9" and python_version <= "3.10") and extra == 'all'
+Requires-Dist: nibabel; extra == "all"
+Requires-Dist: ninja; extra == "all"
+Requires-Dist: scikit-image>=0.14.2; extra == "all"
+Requires-Dist: pillow; extra == "all"
+Requires-Dist: tensorboard; extra == "all"
+Requires-Dist: gdown>=4.7.3; extra == "all"
+Requires-Dist: pytorch-ignite==0.4.11; extra == "all"
+Requires-Dist: torchvision; extra == "all"
+Requires-Dist: itk>=5.2; extra == "all"
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+Requires-Dist: pyyaml; extra == "all"
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+Requires-Dist: pydicom; extra == "all"
+Requires-Dist: h5py; extra == "all"
+Requires-Dist: nni; extra == "all"
+Requires-Dist: optuna; extra == "all"
+Requires-Dist: onnx>=1.13.0; extra == "all"
+Requires-Dist: zarr; extra == "all"
+Requires-Dist: lpips==0.1.4; extra == "all"
+Requires-Dist: nvidia-ml-py; extra == "all"
+Requires-Dist: huggingface-hub; extra == "all"
+Requires-Dist: pyamg>=5.0.0; extra == "all"
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+Requires-Dist: cucim-cu12; (python_version >= "3.9" and python_version <= "3.10") and extra == "all"
 Provides-Extra: clearml
-Requires-Dist: clearml ; extra == 'clearml'
+Requires-Dist: clearml; extra == "clearml"
 Provides-Extra: cucim
-Requires-Dist: cucim-cu12 ; extra == 'cucim'
+Requires-Dist: cucim-cu12; extra == "cucim"
 Provides-Extra: einops
-Requires-Dist: einops ; extra == 'einops'
+Requires-Dist: einops; extra == "einops"
 Provides-Extra: fire
-Requires-Dist: fire ; extra == 'fire'
+Requires-Dist: fire; extra == "fire"
 Provides-Extra: gdown
-Requires-Dist: gdown >=4.7.3 ; extra == 'gdown'
+Requires-Dist: gdown>=4.7.3; extra == "gdown"
 Provides-Extra: h5py
-Requires-Dist: h5py ; extra == 'h5py'
+Requires-Dist: h5py; extra == "h5py"
 Provides-Extra: huggingface_hub
-Requires-Dist: huggingface-hub ; extra == 'huggingface_hub'
+Requires-Dist: huggingface-hub; extra == "huggingface-hub"
 Provides-Extra: ignite
-Requires-Dist: pytorch-ignite ==0.4.11 ; extra == 'ignite'
+Requires-Dist: pytorch-ignite==0.4.11; extra == "ignite"
 Provides-Extra: imagecodecs
-Requires-Dist: imagecodecs ; extra == 'imagecodecs'
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 Provides-Extra: itk
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 <p align="center">
   <img src="https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/MONAI-logo-color.png" width="50%" alt='project-monai'>