monai-weekly 1.5.dev2510__tar.gz → 1.5.dev2512__tar.gz

{monai_weekly-1.5.dev2510/monai_weekly.egg-info → monai_weekly-1.5.dev2512}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.5.dev2510
+Version: 1.5.dev2512
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium
@@ -156,6 +156,7 @@ Provides-Extra: huggingface-hub
 Requires-Dist: huggingface_hub; extra == "huggingface-hub"
 Provides-Extra: pyamg
 Requires-Dist: pyamg>=5.0.0; extra == "pyamg"
+Dynamic: license-file
 
 <p align="center">
   <img src="https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/MONAI-logo-color.png" width="50%" alt='project-monai'>

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512}/monai/__init__.py

@@ -136,4 +136,4 @@ except BaseException:
 
     if MONAIEnvVars.debug():
         raise
-__commit_id__ = "7c26e5af385eb5f7a813fa405c6f3fc87b7511fa"
+__commit_id__ = "5c5ca232a1ccf0e7eae99dd386b8b37472d8aa4c"

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512}/monai/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-03-09T02:16:22+0000",
+ "date": "2025-03-23T02:31:42+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "19fadf962d87a21e1d0edf8d72299e82f7611140",
- "version": "1.5.dev2510"
+ "full-revisionid": "e4701e24c97d1f8c7ba40777c238cdfe14b04581",
+ "version": "1.5.dev2512"
 }
 '''  # END VERSION_JSON
 

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512}/monai/apps/generation/maisi/networks/autoencoderkl_maisi.py

@@ -232,6 +232,10 @@ class MaisiConvolution(nn.Module):
         if self.print_info:
             logger.info(f"Number of splits: {self.num_splits}")
 
+        if self.dim_split <= 1 and self.num_splits <= 1:
+            x = self.conv(x)
+            return x
+
         # compute size of splits
         l = x.size(self.dim_split + 2)
         split_size = l // self.num_splits

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512}/monai/data/utils.py

@@ -1473,7 +1473,7 @@ def convert_tables_to_dicts(
     # parse row indices
     rows: list[int | str] = []
     if row_indices is None:
-        rows = slice(df.shape[0])  # type: ignore
+        rows = df.index.tolist()
     else:
         for i in row_indices:
             if isinstance(i, (tuple, list)):

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512}/monai/inferers/inferer.py

@@ -39,7 +39,7 @@ from monai.networks.nets import (
     SPADEAutoencoderKL,
     SPADEDiffusionModelUNet,
 )
-from monai.networks.schedulers import Scheduler
+from monai.networks.schedulers import RFlowScheduler, Scheduler
 from monai.transforms import CenterSpatialCrop, SpatialPad
 from monai.utils import BlendMode, Ordering, PatchKeys, PytorchPadMode, ensure_tuple, optional_import
 from monai.visualize import CAM, GradCAM, GradCAMpp
@@ -859,12 +859,18 @@ class DiffusionInferer(Inferer):
         if not scheduler:
             scheduler = self.scheduler
         image = input_noise
+
+        all_next_timesteps = torch.cat((scheduler.timesteps[1:], torch.tensor([0], dtype=scheduler.timesteps.dtype)))
         if verbose and has_tqdm:
-            progress_bar = tqdm(scheduler.timesteps)
+            progress_bar = tqdm(
+                zip(scheduler.timesteps, all_next_timesteps),
+                total=min(len(scheduler.timesteps), len(all_next_timesteps)),
+            )
         else:
-            progress_bar = iter(scheduler.timesteps)
+            progress_bar = iter(zip(scheduler.timesteps, all_next_timesteps))
         intermediates = []
-        for t in progress_bar:
+
+        for t, next_t in progress_bar:
             # 1. predict noise model_output
             diffusion_model = (
                 partial(diffusion_model, seg=seg)
@@ -882,9 +888,13 @@ class DiffusionInferer(Inferer):
                 )
 
             # 2. compute previous image: x_t -> x_t-1
-            image, _ = scheduler.step(model_output, t, image)  # type: ignore[operator]
+            if not isinstance(scheduler, RFlowScheduler):
+                image, _ = scheduler.step(model_output, t, image)  # type: ignore
+            else:
+                image, _ = scheduler.step(model_output, t, image, next_t)  # type: ignore
             if save_intermediates and t % intermediate_steps == 0:
                 intermediates.append(image)
+
         if save_intermediates:
             return image, intermediates
         else:
@@ -1392,12 +1402,18 @@ class ControlNetDiffusionInferer(DiffusionInferer):
         if not scheduler:
             scheduler = self.scheduler
         image = input_noise
+
+        all_next_timesteps = torch.cat((scheduler.timesteps[1:], torch.tensor([0], dtype=scheduler.timesteps.dtype)))
         if verbose and has_tqdm:
-            progress_bar = tqdm(scheduler.timesteps)
+            progress_bar = tqdm(
+                zip(scheduler.timesteps, all_next_timesteps),
+                total=min(len(scheduler.timesteps), len(all_next_timesteps)),
+            )
         else:
-            progress_bar = iter(scheduler.timesteps)
+            progress_bar = iter(zip(scheduler.timesteps, all_next_timesteps))
         intermediates = []
-        for t in progress_bar:
+
+        for t, next_t in progress_bar:
             diffuse = diffusion_model
             if isinstance(diffusion_model, SPADEDiffusionModelUNet):
                 diffuse = partial(diffusion_model, seg=seg)
@@ -1436,7 +1452,11 @@ class ControlNetDiffusionInferer(DiffusionInferer):
                 )
 
             # 3. compute previous image: x_t -> x_t-1
-            image, _ = scheduler.step(model_output, t, image)  # type: ignore[operator]
+            if not isinstance(scheduler, RFlowScheduler):
+                image, _ = scheduler.step(model_output, t, image)  # type: ignore
+            else:
+                image, _ = scheduler.step(model_output, t, image, next_t)  # type: ignore
+
             if save_intermediates and t % intermediate_steps == 0:
                 intermediates.append(image)
         if save_intermediates:

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512}/monai/networks/schedulers/__init__.py

@@ -14,4 +14,5 @@ from __future__ import annotations
 from .ddim import DDIMScheduler
 from .ddpm import DDPMScheduler
 from .pndm import PNDMScheduler
+from .rectified_flow import RFlowScheduler
 from .scheduler import NoiseSchedules, Scheduler

monai_weekly-1.5.dev2512/monai/networks/schedulers/rectified_flow.py

@@ -0,0 +1,322 @@
+# 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.
+#
+# =========================================================================
+# Adapted from https://github.com/hpcaitech/Open-Sora/blob/main/opensora/schedulers/rf/rectified_flow.py
+# which has the following license:
+# https://github.com/hpcaitech/Open-Sora/blob/main/LICENSE
+# 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 Union
+
+import numpy as np
+import torch
+from torch.distributions import LogisticNormal
+
+from monai.utils import StrEnum
+
+from .ddpm import DDPMPredictionType
+from .scheduler import Scheduler
+
+
+class RFlowPredictionType(StrEnum):
+    """
+    Set of valid prediction type names for the RFlow scheduler's `prediction_type` argument.
+
+    v_prediction: velocity prediction, see section 2.4 https://imagen.research.google/video/paper.pdf
+    """
+
+    V_PREDICTION = DDPMPredictionType.V_PREDICTION
+
+
+def timestep_transform(
+    t, input_img_size_numel, base_img_size_numel=32 * 32 * 32, scale=1.0, num_train_timesteps=1000, spatial_dim=3
+):
+    """
+    Applies a transformation to the timestep based on image resolution scaling.
+
+    Args:
+        t (torch.Tensor): The original timestep(s).
+        input_img_size_numel (torch.Tensor): The input image's size (H * W * D).
+        base_img_size_numel (int): reference H*W*D size, usually smaller than input_img_size_numel.
+        scale (float): Scaling factor for the transformation.
+        num_train_timesteps (int): Total number of training timesteps.
+        spatial_dim (int): Number of spatial dimensions in the image.
+
+    Returns:
+        torch.Tensor: Transformed timestep(s).
+    """
+    t = t / num_train_timesteps
+    ratio_space = (input_img_size_numel / base_img_size_numel) ** (1.0 / spatial_dim)
+
+    ratio = ratio_space * scale
+    new_t = ratio * t / (1 + (ratio - 1) * t)
+
+    new_t = new_t * num_train_timesteps
+    return new_t
+
+
+class RFlowScheduler(Scheduler):
+    """
+    A rectified flow scheduler for guiding the diffusion process in a generative model.
+
+    Supports uniform and logit-normal sampling methods, timestep transformation for
+    different resolutions, and noise addition during diffusion.
+
+    Args:
+        num_train_timesteps (int): Total number of training timesteps.
+        use_discrete_timesteps (bool): Whether to use discrete timesteps.
+        sample_method (str): Training time step sampling method ('uniform' or 'logit-normal').
+        loc (float): Location parameter for logit-normal distribution, used only if sample_method='logit-normal'.
+        scale (float): Scale parameter for logit-normal distribution, used only if sample_method='logit-normal'.
+        use_timestep_transform (bool): Whether to apply timestep transformation.
+            If true, there will be more inference timesteps at early(noisy) stages for larger image volumes.
+        transform_scale (float): Scaling factor for timestep transformation, used only if use_timestep_transform=True.
+        steps_offset (int): Offset added to computed timesteps, used only if use_timestep_transform=True.
+        base_img_size_numel (int): Reference image volume size for scaling, used only if use_timestep_transform=True.
+        spatial_dim (int): 2 or 3, incidcating 2D or 3D images, used only if use_timestep_transform=True.
+
+    Example:
+
+        .. code-block:: python
+
+            # define a scheduler
+            noise_scheduler = RFlowScheduler(
+                num_train_timesteps = 1000,
+                use_discrete_timesteps = True,
+                sample_method = 'logit-normal',
+                use_timestep_transform = True,
+                base_img_size_numel = 32 * 32 * 32,
+                spatial_dim = 3
+            )
+
+            # during training
+            inputs = torch.ones(2,4,64,64,32)
+            noise = torch.randn_like(inputs)
+            timesteps = noise_scheduler.sample_timesteps(inputs)
+            noisy_inputs = noise_scheduler.add_noise(original_samples=inputs, noise=noise, timesteps=timesteps)
+            predicted_velocity = diffusion_unet(
+                x=noisy_inputs,
+                timesteps=timesteps
+            )
+            loss = loss_l1(predicted_velocity, (inputs - noise))
+
+            # during inference
+            noisy_inputs = torch.randn(2,4,64,64,32)
+            input_img_size_numel = torch.prod(torch.tensor(noisy_inputs.shape[-3:])
+            noise_scheduler.set_timesteps(
+                num_inference_steps=30, input_img_size_numel=input_img_size_numel)
+            )
+            all_next_timesteps = torch.cat(
+                (noise_scheduler.timesteps[1:], torch.tensor([0], dtype=noise_scheduler.timesteps.dtype))
+            )
+            for t, next_t in tqdm(
+                zip(noise_scheduler.timesteps, all_next_timesteps),
+                total=min(len(noise_scheduler.timesteps), len(all_next_timesteps)),
+            ):
+                predicted_velocity = diffusion_unet(
+                    x=noisy_inputs,
+                    timesteps=timesteps
+                )
+                noisy_inputs, _ = noise_scheduler.step(predicted_velocity, t, noisy_inputs, next_t)
+            final_output = noisy_inputs
+    """
+
+    def __init__(
+        self,
+        num_train_timesteps: int = 1000,
+        use_discrete_timesteps: bool = True,
+        sample_method: str = "uniform",
+        loc: float = 0.0,
+        scale: float = 1.0,
+        use_timestep_transform: bool = False,
+        transform_scale: float = 1.0,
+        steps_offset: int = 0,
+        base_img_size_numel: int = 32 * 32 * 32,
+        spatial_dim: int = 3,
+    ):
+        # rectified flow only accepts velocity prediction
+        self.prediction_type = RFlowPredictionType.V_PREDICTION
+
+        self.num_train_timesteps = num_train_timesteps
+        self.use_discrete_timesteps = use_discrete_timesteps
+        self.base_img_size_numel = base_img_size_numel
+        self.spatial_dim = spatial_dim
+
+        # sample method
+        if sample_method not in ["uniform", "logit-normal"]:
+            raise ValueError(
+                f"sample_method = {sample_method}, which has to be chosen from ['uniform', 'logit-normal']."
+            )
+        self.sample_method = sample_method
+        if sample_method == "logit-normal":
+            self.distribution = LogisticNormal(torch.tensor([loc]), torch.tensor([scale]))
+            self.sample_t = lambda x: self.distribution.sample((x.shape[0],))[:, 0].to(x.device)
+
+        # timestep transform
+        self.use_timestep_transform = use_timestep_transform
+        self.transform_scale = transform_scale
+        self.steps_offset = steps_offset
+
+    def add_noise(self, original_samples: torch.Tensor, noise: torch.Tensor, timesteps: torch.Tensor) -> torch.Tensor:
+        """
+        Add noise to the original samples.
+
+        Args:
+            original_samples: original samples
+            noise: noise to add to samples
+            timesteps: timesteps tensor with shape of (N,), indicating the timestep to be computed for each sample.
+
+        Returns:
+            noisy_samples: sample with added noise
+        """
+        timepoints: torch.Tensor = timesteps.float() / self.num_train_timesteps
+        timepoints = 1 - timepoints  # [1,1/1000]
+
+        # expand timepoint to noise shape
+        if noise.ndim == 5:
+            timepoints = timepoints[..., None, None, None, None].expand(-1, *noise.shape[1:])
+        elif noise.ndim == 4:
+            timepoints = timepoints[..., None, None, None].expand(-1, *noise.shape[1:])
+        else:
+            raise ValueError(f"noise tensor has to be 4D or 5D tensor, yet got shape of {noise.shape}")
+
+        noisy_samples: torch.Tensor = timepoints * original_samples + (1 - timepoints) * noise
+
+        return noisy_samples
+
+    def set_timesteps(
+        self,
+        num_inference_steps: int,
+        device: str | torch.device | None = None,
+        input_img_size_numel: int | None = None,
+    ) -> None:
+        """
+        Sets the discrete timesteps used for the diffusion chain. Supporting function to be run before inference.
+
+        Args:
+            num_inference_steps: number of diffusion steps used when generating samples with a pre-trained model.
+            device: target device to put the data.
+            input_img_size_numel: int, H*W*D of the image, used with self.use_timestep_transform is True.
+        """
+        if num_inference_steps > self.num_train_timesteps or num_inference_steps < 1:
+            raise ValueError(
+                f"`num_inference_steps`: {num_inference_steps} should be at least 1, "
+                "and cannot be larger than `self.num_train_timesteps`:"
+                f" {self.num_train_timesteps} as the unet model trained with this scheduler can only handle"
+                f" maximal {self.num_train_timesteps} timesteps."
+            )
+
+        self.num_inference_steps = num_inference_steps
+        # prepare timesteps
+        timesteps = [
+            (1.0 - i / self.num_inference_steps) * self.num_train_timesteps for i in range(self.num_inference_steps)
+        ]
+        if self.use_discrete_timesteps:
+            timesteps = [int(round(t)) for t in timesteps]
+        if self.use_timestep_transform:
+            timesteps = [
+                timestep_transform(
+                    t,
+                    input_img_size_numel=input_img_size_numel,
+                    base_img_size_numel=self.base_img_size_numel,
+                    num_train_timesteps=self.num_train_timesteps,
+                    spatial_dim=self.spatial_dim,
+                )
+                for t in timesteps
+            ]
+        timesteps_np = np.array(timesteps).astype(np.float16)
+        if self.use_discrete_timesteps:
+            timesteps_np = timesteps_np.astype(np.int64)
+        self.timesteps = torch.from_numpy(timesteps_np).to(device)
+        self.timesteps += self.steps_offset
+
+    def sample_timesteps(self, x_start):
+        """
+        Randomly samples training timesteps using the chosen sampling method.
+
+        Args:
+            x_start (torch.Tensor): The input tensor for sampling.
+
+        Returns:
+            torch.Tensor: Sampled timesteps.
+        """
+        if self.sample_method == "uniform":
+            t = torch.rand((x_start.shape[0],), device=x_start.device) * self.num_train_timesteps
+        elif self.sample_method == "logit-normal":
+            t = self.sample_t(x_start) * self.num_train_timesteps
+
+        if self.use_discrete_timesteps:
+            t = t.long()
+
+        if self.use_timestep_transform:
+            input_img_size_numel = torch.prod(torch.tensor(x_start.shape[2:]))
+            t = timestep_transform(
+                t,
+                input_img_size_numel=input_img_size_numel,
+                base_img_size_numel=self.base_img_size_numel,
+                num_train_timesteps=self.num_train_timesteps,
+                spatial_dim=len(x_start.shape) - 2,
+            )
+
+        return t
+
+    def step(
+        self, model_output: torch.Tensor, timestep: int, sample: torch.Tensor, next_timestep: Union[int, None] = None
+    ) -> tuple[torch.Tensor, torch.Tensor]:
+        """
+        Predicts the next sample in the diffusion process.
+
+        Args:
+            model_output (torch.Tensor): Output from the trained diffusion model.
+            timestep (int): Current timestep in the diffusion chain.
+            sample (torch.Tensor): Current sample in the process.
+            next_timestep (Union[int, None]): Optional next timestep.
+
+        Returns:
+            tuple[torch.Tensor, torch.Tensor]: Predicted sample at the next step and additional info.
+        """
+        # Ensure num_inference_steps exists and is a valid integer
+        if not hasattr(self, "num_inference_steps") or not isinstance(self.num_inference_steps, int):
+            raise AttributeError(
+                "num_inference_steps is missing or not an integer in the class."
+                "Please run self.set_timesteps(num_inference_steps,device,input_img_size_numel) to set it."
+            )
+
+        v_pred = model_output
+
+        if next_timestep is not None:
+            next_timestep = int(next_timestep)
+            dt: float = (
+                float(timestep - next_timestep) / self.num_train_timesteps
+            )  # Now next_timestep is guaranteed to be int
+        else:
+            dt = (
+                1.0 / float(self.num_inference_steps) if self.num_inference_steps > 0 else 0.0
+            )  # Avoid division by zero
+
+        pred_post_sample = sample + v_pred * dt
+        pred_original_sample = sample + v_pred * timestep / self.num_train_timesteps
+
+        return pred_post_sample, pred_original_sample

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512}/monai/utils/misc.py

@@ -546,7 +546,7 @@ class MONAIEnvVars:
 
     @staticmethod
     def algo_hash() -> str | None:
-        return os.environ.get("MONAI_ALGO_HASH", "c970bdf")
+        return os.environ.get("MONAI_ALGO_HASH", "c108ea9")
 
     @staticmethod
     def trace_transform() -> str | None:

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512/monai_weekly.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: monai-weekly
-Version: 1.5.dev2510
+Version: 1.5.dev2512
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium
@@ -156,6 +156,7 @@ Provides-Extra: huggingface-hub
 Requires-Dist: huggingface_hub; extra == "huggingface-hub"
 Provides-Extra: pyamg
 Requires-Dist: pyamg>=5.0.0; extra == "pyamg"
+Dynamic: license-file
 
 <p align="center">
   <img src="https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/MONAI-logo-color.png" width="50%" alt='project-monai'>

{monai_weekly-1.5.dev2510 → monai_weekly-1.5.dev2512}/monai_weekly.egg-info/SOURCES.txt

@@ -352,6 +352,7 @@ monai/networks/schedulers/__init__.py
 monai/networks/schedulers/ddim.py
 monai/networks/schedulers/ddpm.py
 monai/networks/schedulers/pndm.py
+monai/networks/schedulers/rectified_flow.py
 monai/networks/schedulers/scheduler.py
 monai/optimizers/__init__.py
 monai/optimizers/lr_finder.py
@@ -826,6 +827,7 @@ tests/networks/schedulers/__init__.py
 tests/networks/schedulers/test_scheduler_ddim.py
 tests/networks/schedulers/test_scheduler_ddpm.py
 tests/networks/schedulers/test_scheduler_pndm.py
+tests/networks/schedulers/test_scheduler_rflow.py
 tests/networks/utils/__init__.py
 tests/networks/utils/test_copy_model_state.py
 tests/networks/utils/test_eval_mode.py