monai-weekly 1.4.dev2426__py3-none-any.whl → 1.4.dev2427__py3-none-any.whl

monai/apps/generation/maisi/utils/morphological_ops.py

@@ -0,0 +1,170 @@
+# 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.
+
+from __future__ import annotations
+
+from typing import Sequence
+
+import torch
+import torch.nn.functional as F
+from torch import Tensor
+
+from monai.config import NdarrayOrTensor
+from monai.utils import convert_data_type, convert_to_dst_type, ensure_tuple_rep
+
+
+def erode(mask: NdarrayOrTensor, filter_size: int | Sequence[int] = 3, pad_value: float = 1.0) -> NdarrayOrTensor:
+    """
+    Erode 2D/3D binary mask.
+
+    Args:
+        mask: input 2D/3D binary mask, [N,C,M,N] or [N,C,M,N,P] torch tensor or ndarray.
+        filter_size: erosion filter size, has to be odd numbers, default to be 3.
+        pad_value: the filled value for padding. We need to pad the input before filtering
+                   to keep the output with the same size as input. Usually use default value
+                   and not changed.
+
+    Return:
+        eroded mask, same shape and data type as input.
+
+    Example:
+
+        .. code-block:: python
+
+            # define a naive mask
+            mask = torch.zeros(3,2,3,3,3)
+            mask[:,:,1,1,1] = 1.0
+            filter_size = 3
+            erode_result = erode(mask, filter_size)  # expect torch.zeros(3,2,3,3,3)
+            dilate_result = dilate(mask, filter_size)  # expect torch.ones(3,2,3,3,3)
+    """
+    mask_t, *_ = convert_data_type(mask, torch.Tensor)
+    res_mask_t = erode_t(mask_t, filter_size=filter_size, pad_value=pad_value)
+    res_mask: NdarrayOrTensor
+    res_mask, *_ = convert_to_dst_type(src=res_mask_t, dst=mask)
+    return res_mask
+
+
+def dilate(mask: NdarrayOrTensor, filter_size: int | Sequence[int] = 3, pad_value: float = 0.0) -> NdarrayOrTensor:
+    """
+    Dilate 2D/3D binary mask.
+
+    Args:
+        mask: input 2D/3D binary mask, [N,C,M,N] or [N,C,M,N,P] torch tensor or ndarray.
+        filter_size: dilation filter size, has to be odd numbers, default to be 3.
+        pad_value: the filled value for padding. We need to pad the input before filtering
+                   to keep the output with the same size as input. Usually use default value
+                   and not changed.
+
+    Return:
+        dilated mask, same shape and data type as input.
+
+    Example:
+
+        .. code-block:: python
+
+            # define a naive mask
+            mask = torch.zeros(3,2,3,3,3)
+            mask[:,:,1,1,1] = 1.0
+            filter_size = 3
+            erode_result = erode(mask,filter_size) # expect torch.zeros(3,2,3,3,3)
+            dilate_result = dilate(mask,filter_size) # expect torch.ones(3,2,3,3,3)
+    """
+    mask_t, *_ = convert_data_type(mask, torch.Tensor)
+    res_mask_t = dilate_t(mask_t, filter_size=filter_size, pad_value=pad_value)
+    res_mask: NdarrayOrTensor
+    res_mask, *_ = convert_to_dst_type(src=res_mask_t, dst=mask)
+    return res_mask
+
+
+def get_morphological_filter_result_t(mask_t: Tensor, filter_size: int | Sequence[int], pad_value: float) -> Tensor:
+    """
+    Apply a morphological filter to a 2D/3D binary mask tensor.
+
+    Args:
+        mask_t: input 2D/3D binary mask, [N,C,M,N] or [N,C,M,N,P] torch tensor.
+        filter_size: morphological filter size, has to be odd numbers.
+        pad_value: the filled value for padding. We need to pad the input before filtering
+                   to keep the output with the same size as input.
+
+    Return:
+        Tensor: Morphological filter result mask, same shape as input.
+    """
+    spatial_dims = len(mask_t.shape) - 2
+    if spatial_dims not in [2, 3]:
+        raise ValueError(
+            f"spatial_dims must be either 2 or 3, "
+            f"got spatial_dims={spatial_dims} for mask tensor with shape of {mask_t.shape}."
+        )
+
+    # Define the structuring element
+    filter_size = ensure_tuple_rep(filter_size, spatial_dims)
+    if any(size % 2 == 0 for size in filter_size):
+        raise ValueError(f"All dimensions in filter_size must be odd numbers, got {filter_size}.")
+
+    structuring_element = torch.ones((mask_t.shape[1], mask_t.shape[1]) + filter_size).to(mask_t.device)
+
+    # Pad the input tensor to handle border pixels
+    # Calculate padding size
+    pad_size = [size // 2 for size in filter_size for _ in range(2)]
+
+    input_padded = F.pad(mask_t.float(), pad_size, mode="constant", value=pad_value)
+
+    # Apply filter operation
+    conv_fn = F.conv2d if spatial_dims == 2 else F.conv3d
+    output = conv_fn(input_padded, structuring_element, padding=0) / torch.sum(structuring_element[0, ...])
+
+    return output
+
+
+def erode_t(mask_t: Tensor, filter_size: int | Sequence[int] = 3, pad_value: float = 1.0) -> Tensor:
+    """
+    Erode 2D/3D binary mask with data type as torch tensor.
+
+    Args:
+        mask_t: input 2D/3D binary mask, [N,C,M,N] or [N,C,M,N,P] torch tensor.
+        filter_size: erosion filter size, has to be odd numbers, default to be 3.
+        pad_value: the filled value for padding. We need to pad the input before filtering
+                   to keep the output with the same size as input. Usually use default value
+                   and not changed.
+
+    Return:
+        Tensor: eroded mask, same shape as input.
+    """
+
+    output = get_morphological_filter_result_t(mask_t, filter_size, pad_value)
+
+    # Set output values based on the minimum value within the structuring element
+    output = torch.where(torch.abs(output - 1.0) < 1e-7, 1.0, 0.0)
+
+    return output
+
+
+def dilate_t(mask_t: Tensor, filter_size: int | Sequence[int] = 3, pad_value: float = 0.0) -> Tensor:
+    """
+    Dilate 2D/3D binary mask with data type as torch tensor.
+
+    Args:
+        mask_t: input 2D/3D binary mask, [N,C,M,N] or [N,C,M,N,P] torch tensor.
+        filter_size: dilation filter size, has to be odd numbers, default to be 3.
+        pad_value: the filled value for padding. We need to pad the input before filtering
+                   to keep the output with the same size as input. Usually use default value
+                   and not changed.
+
+    Return:
+        Tensor: dilated mask, same shape as input.
+    """
+    output = get_morphological_filter_result_t(mask_t, filter_size, pad_value)
+
+    # Set output values based on the minimum value within the structuring element
+    output = torch.where(output > 0, 1.0, 0.0)
+
+    return output

monai/data/torchscript_utils.py

@@ -116,7 +116,7 @@ def load_net_with_metadata(
     Returns:
         Triple containing loaded object, metadata dict, and extra files dict containing other file data if present
     """
-    extra_files = {f: "" for f in more_extra_files}
+    extra_files = dict.fromkeys(more_extra_files, "")
     extra_files[METADATA_FILENAME] = ""
 
     jit_obj = torch.jit.load(filename_prefix_or_stream, map_location, extra_files)

monai/data/ultrasound_confidence_map.py

@@ -19,10 +19,10 @@ from monai.utils import min_version, optional_import
 __all__ = ["UltrasoundConfidenceMap"]
 
 cv2, _ = optional_import("cv2")
-csc_matrix, _ = optional_import("scipy.sparse", "1.7.1", min_version, "csc_matrix")
-spsolve, _ = optional_import("scipy.sparse.linalg", "1.7.1", min_version, "spsolve")
-cg, _ = optional_import("scipy.sparse.linalg", "1.7.1", min_version, "cg")
-hilbert, _ = optional_import("scipy.signal", "1.7.1", min_version, "hilbert")
+csc_matrix, _ = optional_import("scipy.sparse", "1.12.0", min_version, "csc_matrix")
+spsolve, _ = optional_import("scipy.sparse.linalg", "1.12.0", min_version, "spsolve")
+cg, _ = optional_import("scipy.sparse.linalg", "1.12.0", min_version, "cg")
+hilbert, _ = optional_import("scipy.signal", "1.12.0", min_version, "hilbert")
 ruge_stuben_solver, _ = optional_import("pyamg", "5.0.0", min_version, "ruge_stuben_solver")
 
 
@@ -285,7 +285,7 @@ class UltrasoundConfidenceMap:
             lap_sparse = lap.tocsr()
             ml = ruge_stuben_solver(lap_sparse, coarse_solver="pinv")
             m = ml.aspreconditioner(cycle="V")
-            x, _ = cg(lap, rhs, tol=self.cg_tol, maxiter=self.cg_maxiter, M=m)
+            x, _ = cg(lap, rhs, rtol=self.cg_tol, maxiter=self.cg_maxiter, M=m)
         else:
             x = spsolve(lap, rhs)
 

monai/optimizers/lr_finder.py

@@ -524,7 +524,7 @@ class LearningRateFinder:
         # Plot the LR with steepest gradient
         if steepest_lr:
             lr_at_steepest_grad, loss_at_steepest_grad = self.get_steepest_gradient(skip_start, skip_end)
-            if lr_at_steepest_grad is not None:
+            if lr_at_steepest_grad is not None and loss_at_steepest_grad is not None:
                 ax.scatter(
                     lr_at_steepest_grad,
                     loss_at_steepest_grad,

monai/utils/misc.py

@@ -24,7 +24,6 @@ import types
 import warnings
 from ast import literal_eval
 from collections.abc import Callable, Iterable, Sequence
-from distutils.util import strtobool
 from math import log10
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, TypeVar, cast, overload
@@ -78,6 +77,25 @@ __all__ = [
     "run_cmd",
 ]
 
+
+def _strtobool(val: str) -> bool:
+    """
+    Replaces deprecated (pre python 3.12)
+    distutils strtobool function.
+
+    True values are y, yes, t, true, on and 1;
+    False values are n, no, f, false, off and 0.
+    Raises ValueError if val is anything else.
+    """
+    val = val.lower()
+    if val in ("y", "yes", "t", "true", "on", "1"):
+        return True
+    elif val in ("n", "no", "f", "false", "off", "0"):
+        return False
+    else:
+        raise ValueError(f"invalid truth value {val}")
+
+
 _seed = None
 _flag_deterministic = torch.backends.cudnn.deterministic
 _flag_cudnn_benchmark = torch.backends.cudnn.benchmark
@@ -400,7 +418,7 @@ def list_to_dict(items):
                 d[key] = literal_eval(value)
             except ValueError:
                 try:
-                    d[key] = bool(strtobool(str(value)))
+                    d[key] = bool(_strtobool(str(value)))
                 except ValueError:
                     d[key] = value
     return d

{monai_weekly-1.4.dev2426.dist-info → monai_weekly-1.4.dev2427.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: monai-weekly
-Version: 1.4.dev2426
+Version: 1.4.dev2427
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium
@@ -35,7 +35,6 @@ Provides-Extra: all
 Requires-Dist: nibabel ; extra == 'all'
 Requires-Dist: ninja ; extra == 'all'
 Requires-Dist: scikit-image >=0.14.2 ; extra == 'all'
-Requires-Dist: scipy >=1.7.1 ; extra == 'all'
 Requires-Dist: pillow ; extra == 'all'
 Requires-Dist: tensorboard ; extra == 'all'
 Requires-Dist: gdown >=4.7.3 ; extra == 'all'
@@ -70,6 +69,7 @@ Requires-Dist: huggingface-hub ; extra == 'all'
 Requires-Dist: pyamg >=5.0.0 ; extra == 'all'
 Requires-Dist: transformers <4.41.0,>=4.36.0 ; (python_version <= "3.10") and extra == 'all'
 Requires-Dist: onnxruntime ; (python_version <= "3.10") and extra == 'all'
+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'
 Provides-Extra: clearml
 Requires-Dist: clearml ; extra == 'clearml'
@@ -131,7 +131,7 @@ Requires-Dist: nvidia-ml-py ; extra == 'pynvml'
 Provides-Extra: pyyaml
 Requires-Dist: pyyaml ; extra == 'pyyaml'
 Provides-Extra: scipy
-Requires-Dist: scipy >=1.7.1 ; extra == 'scipy'
+Requires-Dist: scipy >=1.12.0 ; (python_version >= "3.9") and extra == 'scipy'
 Provides-Extra: skimage
 Requires-Dist: scikit-image >=0.14.2 ; extra == 'skimage'
 Provides-Extra: tensorboard

{monai_weekly-1.4.dev2426.dist-info → monai_weekly-1.4.dev2427.dist-info}/RECORD

@@ -1,5 +1,5 @@
-monai/__init__.py,sha256=ImQNW_ROu1w5VUIP1j9o-vv9jfMvOCSuTsyZm6eHluE,2722
-monai/_version.py,sha256=fknoI1rCBz7kKd3KcjzyJ-QgcWxoZW6hO4Vxvn5iVxE,503
+monai/__init__.py,sha256=eoyjvFJSEfWDlE4q_HInTk09cmQ9viq3hhYZW5SyZEk,2722
+monai/_version.py,sha256=bhGlwE1LiuJLSjwhd1Em13cuIoeS-w6hRghkMeyBm6k,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
@@ -46,6 +46,14 @@ monai/apps/detection/utils/box_selector.py,sha256=uXI0YrhugYR68xYshRs5JpPTT1nL3Q
 monai/apps/detection/utils/detector_utils.py,sha256=pU7bOzH-ay9Lnzu1aHCrIwlaGVf5xj13E7Somx_vFnk,10306
 monai/apps/detection/utils/hard_negative_sampler.py,sha256=PywdXkFIAdudmp3W8JWM_CcLC3BKWQh5x1y0tuuokcg,13890
 monai/apps/detection/utils/predict_utils.py,sha256=6j7U-7pLtbmgE6SXKR_MVImc67-M8WtzQkT89cCVsK8,5818
+monai/apps/generation/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
+monai/apps/generation/maisi/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
+monai/apps/generation/maisi/networks/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
+monai/apps/generation/maisi/networks/autoencoderkl_maisi.py,sha256=U6vShAKr9BR3Mvc5h4CcspL8iO9sl3tHSmTcPN-A64Q,35481
+monai/apps/generation/maisi/networks/controlnet_maisi.py,sha256=2z5ycY_3899C2TQQNUALRW1Wf2OQVlfAmZSv5dycT2I,7734
+monai/apps/generation/maisi/networks/diffusion_model_unet_maisi.py,sha256=oJvP7jKLW_3vOC_HMufI0AY__c8TUd6r_E9bklzMOVE,19237
+monai/apps/generation/maisi/utils/__init__.py,sha256=s9djSd6kvViPnFvMR11Dgd30Lv4oY6FaPJr4ZZJZLq0,573
+monai/apps/generation/maisi/utils/morphological_ops.py,sha256=o1zAHg1EBXmWTZUblWfPDDNAIcdiFsRjvB28Lp_NL5Q,6727
 monai/apps/mmars/__init__.py,sha256=BolpgEi9jNBgrOQd3Kwp-9QQLeWQwQtlN_MJkK1eu5s,726
 monai/apps/mmars/mmars.py,sha256=AYsx5FDmJ0dT0hAkWGYhM470aPIG23PYloHihDZfOKE,13115
 monai/apps/mmars/model_desc.py,sha256=k7WSMRuyQN8xPax8aUmGKiTNZmcVatdqPYCgxDih-x4,9996
@@ -131,8 +139,8 @@ monai/data/samplers.py,sha256=LUCAHy38ddGm67oJJp3W6ITBsDRqyGCrKtYn-pjrWc4,5102
 monai/data/synthetic.py,sha256=H0MaQq2nnYxXEMlvOW1-XoWJWY_VKsgZ75tWLO1aCXg,7375
 monai/data/test_time_augmentation.py,sha256=H1yUph4SkJ-bmKRXS-SRZfNKtWkihR7o4PTUWKuHxOw,9780
 monai/data/thread_buffer.py,sha256=FtJlRwLHQzU9sf3XJk4G7b_-uKXaRQHAOMauc-zWN2Q,8840
-monai/data/torchscript_utils.py,sha256=auz2GtrklxY6PMzvd-i9Kk73uIv0qydpOtzdSfZxrhE,5500
-monai/data/ultrasound_confidence_map.py,sha256=rO63odFjgEju0EkwQWWpb2Oau3Txy7gwWGQuTus32uM,14459
+monai/data/torchscript_utils.py,sha256=KoJinpJiNepP6i-1DDy3-8m1Qg1bPfAZTScmXr0LT6g,5502
+monai/data/ultrasound_confidence_map.py,sha256=pEAp4lr-s00_T9d4IEYSJ5B9VQwf_T7BS9GBx8jw_Sg,14464
 monai/data/utils.py,sha256=WeIcBk7SUy-IOZiPuAp6dFZl9tktJvViDG3wMHaa9dU,66686
 monai/data/video_dataset.py,sha256=mMTZCkgAx_BBoF4HHWcmEuT9zoNoUVPFtPeYYt76t-A,9075
 monai/data/wsi_datasets.py,sha256=Ga5VnOdOXU_tlhdub0ueD4VtWhkQG4IrueXX-abE3bA,18619
@@ -306,7 +314,7 @@ monai/networks/nets/vitautoenc.py,sha256=tTX-JHNl2H4y9e5Wk9rrtR6i_ebJHq90O61DnbB
 monai/networks/nets/vnet.py,sha256=zaJi5kSiTLAuFHThSZfhJvHP6zKh3oBWsTWG-328O_g,10820
 monai/networks/nets/voxelmorph.py,sha256=M6jzGn09wmTd54NeacHLWElug-Iu0ajPS_HtUaLyzDY,20811
 monai/optimizers/__init__.py,sha256=XUL7o9vSL7bZImpxVZqcc1c8MwUMrOZL4nJ-mjAA7yM,796
-monai/optimizers/lr_finder.py,sha256=BooUZ29_w2fzOH6xAKOe6req1VQ78Kf7CrpJZv2fYq8,21954
+monai/optimizers/lr_finder.py,sha256=tbVi6qd-LLI6pENM9cDUv-Hh1HqziO3Wb9aI6JoaPng,21992
 monai/optimizers/lr_scheduler.py,sha256=YPY5MWgCTmExuIOBsVJrgfErkCT1ELBekcH0XeRP6Kk,4082
 monai/optimizers/novograd.py,sha256=dgjyM-WGqrEHsSKNdI3Lw1wJ2YNG3oKCYotfPsDBE80,5677
 monai/optimizers/utils.py,sha256=GVsJsZWO2aAP9IzwhXgca_9gUNHFClup6qG4ZFs42z4,4133
@@ -366,7 +374,7 @@ monai/utils/deprecate_utils.py,sha256=gKeEV4MsI51qeQ5gci2me_C-0e-tDwa3VZzd3XPQqL
 monai/utils/dist.py,sha256=mVaKlBTQJdWAG910sh5pGLEbb_KhRAXV5cPz7amH88Y,8639
 monai/utils/enums.py,sha256=Gdo9WBrFODIYz5zt6c00hGz0bqjUQbhCWsfGSgKlnAU,19674
 monai/utils/jupyter_utils.py,sha256=QqcKhJxzEf6YwM8Ik_HvfVDr7gNfrfzCXdzd2urEH8M,15651
-monai/utils/misc.py,sha256=Mn_sIkTG49yW9wi2MQrnmoxWnvcbonHCxQLG4yWWYDY,30908
+monai/utils/misc.py,sha256=o1eYmYIFRPB71PNvFM4f-3ZhoEmpL2qhl7xneKcDhbY,31380
 monai/utils/module.py,sha256=Uu45ec-NHtccrA1Kv_QL-uxESLcgHLavCg9XelIa6lE,25148
 monai/utils/nvtx.py,sha256=i9JBxR1uhW1ZCgLPLlTx8b907QlXkFzJyTBLMlFjhtU,6876
 monai/utils/profiling.py,sha256=V2_cSHgrcmVF48_G3nUi2-O6fnXsS89nSlb8jj58YLo,15937
@@ -380,8 +388,8 @@ monai/visualize/img2tensorboard.py,sha256=_p5olAefUs6t-y17z0TK32fKxNnUNXVkb0Op1S
 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-1.4.dev2426.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-monai_weekly-1.4.dev2426.dist-info/METADATA,sha256=gaJQgO7GfMPD8kqn4uW3INqCCBSG6KqvWrStKMDcTOw,10890
-monai_weekly-1.4.dev2426.dist-info/WHEEL,sha256=mguMlWGMX-VHnMpKOjjQidIo1ssRlCFu4a4mBpz1s2M,91
-monai_weekly-1.4.dev2426.dist-info/top_level.txt,sha256=UaNwRzLGORdus41Ip446s3bBfViLkdkDsXDo34J2P44,6
-monai_weekly-1.4.dev2426.dist-info/RECORD,,
+monai_weekly-1.4.dev2427.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+monai_weekly-1.4.dev2427.dist-info/METADATA,sha256=a2kPS0TMUt6-axaEsC2VPu79XUqU5ke6YWRuSW2mwuM,10952
+monai_weekly-1.4.dev2427.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
+monai_weekly-1.4.dev2427.dist-info/top_level.txt,sha256=UaNwRzLGORdus41Ip446s3bBfViLkdkDsXDo34J2P44,6
+monai_weekly-1.4.dev2427.dist-info/RECORD,,

{monai_weekly-1.4.dev2426.dist-info → monai_weekly-1.4.dev2427.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.1.1)
+Generator: setuptools (70.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any