medmlx-core 0.1.2__py3-none-any.whl

medmlx_core/THIRD_PARTY_NOTICES.md

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+# Third-party notices
+
+`src/medmlx_core/sliding_window.py` implements algorithms derived from MONAI
+1.6.0 `monai/inferers/utils.py` and `monai/data/utils.py`.
+
+Copyright (c) MONAI Consortium. Licensed under the Apache License, Version 2.0.
+The original license is preserved in `licenses/MONAI_LICENSE`.
+The NumPy/MLX implementation, restricted output/device API, and validation are
+modifications made in this extraction and licensed under Apache-2.0;
+the upstream MONAI portions retain their Apache license.
+
+`src/medmlx_core/channel_last.py` retains layer arithmetic translated from
+MONAI 1.4.0 for the source-pinned released network graphs. The new shared class
+was extracted from RadNN's qualified working source; its model consumers are
+SwinUNETR, FlexibleUNet and HoVer-Net. MONAI Consortium copyright and Apache-2.0
+obligations apply; the full license remains in `licenses/MONAI_LICENSE`.

medmlx_core/__init__.py

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+"""Shared MLX runtime for MedMLX model packages."""
+
+from medmlx_core.checkpoints import (
+    load_torch_checkpoint,
+    mapping_from_pairs,
+    tensor_mapping_from_payload,
+)
+from medmlx_core.errors import (
+    AssetNotReadyError,
+    InvalidInputError,
+    MedmlxError,
+    MissingDependencyError,
+    ModelExecutionError,
+)
+from medmlx_core.layout import (
+    conv3d_weight_to_mlx,
+    conv_transpose3d_weight_to_mlx,
+    require_ncdhw,
+    to_ncdhw,
+    to_ndhwc,
+    tokens_from_ncdhw,
+    tokens_to_ncdhw,
+)
+from medmlx_core.ops import (
+    as_fp32,
+    avg_pool3d_ncdhw,
+    concat_channels_ncdhw,
+    conv3d_ncdhw,
+    conv_transpose3d_ncdhw,
+    group_norm_ncdhw,
+    linear,
+    pad_spatial_trailing_ncdhw,
+    silu,
+    split_conv3d_ncdhw,
+    split_conv_transpose3d_ncdhw,
+    upsample_nearest_ncdhw,
+    upsample_trilinear_ncdhw,
+)
+from medmlx_core.precision import Float32Operators
+from medmlx_core.runtime import (
+    MLX_EXTRA,
+    MlxHostReport,
+    import_mlx,
+    mlx_default_device_name,
+    mlx_peak_memory_bytes,
+    probe_mlx_runtime,
+    require_mlx_device,
+    require_mlx_runtime,
+    reset_mlx_peak_memory,
+)
+from medmlx_core.upsample import deconv2x_ncdhw, upsample_add_ncdhw
+
+__version__ = "0.1.2"
+
+__all__ = [
+    "MLX_EXTRA",
+    "AssetNotReadyError",
+    "Float32Operators",
+    "InvalidInputError",
+    "MedmlxError",
+    "MissingDependencyError",
+    "MlxHostReport",
+    "ModelExecutionError",
+    "as_fp32",
+    "avg_pool3d_ncdhw",
+    "compute_importance_map",
+    "concat_channels_ncdhw",
+    "conv3d_ncdhw",
+    "conv3d_weight_to_mlx",
+    "conv_transpose3d_ncdhw",
+    "conv_transpose3d_weight_to_mlx",
+    "deconv2x_ncdhw",
+    "dense_patch_slices",
+    "group_norm_ncdhw",
+    "import_mlx",
+    "linear",
+    "load_torch_checkpoint",
+    "mapping_from_pairs",
+    "mlx_default_device_name",
+    "mlx_peak_memory_bytes",
+    "pad_spatial_trailing_ncdhw",
+    "probe_mlx_runtime",
+    "require_mlx_device",
+    "require_mlx_runtime",
+    "require_ncdhw",
+    "reset_mlx_peak_memory",
+    "silu",
+    "sliding_window_inference",
+    "split_conv3d_ncdhw",
+    "split_conv_transpose3d_ncdhw",
+    "tensor_mapping_from_payload",
+    "to_ncdhw",
+    "to_ndhwc",
+    "tokens_from_ncdhw",
+    "tokens_to_ncdhw",
+    "upsample_add_ncdhw",
+    "upsample_nearest_ncdhw",
+    "upsample_trilinear_ncdhw",
+]
+
+# The sliding window imports MLX at module level, so load it on first use to
+# keep `import medmlx_core` from importing MLX.
+_LAZY = {
+    "compute_importance_map": "medmlx_core.sliding_window",
+    "dense_patch_slices": "medmlx_core.sliding_window",
+    "sliding_window_inference": "medmlx_core.sliding_window",
+}
+
+
+def __getattr__(name: str) -> object:
+    module = _LAZY.get(name)
+    if module is None:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    from importlib import import_module
+
+    value = getattr(import_module(module), name)
+    globals()[name] = value
+    return value

medmlx_core/channel_last.py

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+"""Channel-last MLX layers shared by standalone medical imaging models."""
+
+from collections.abc import Mapping
+from typing import Any
+
+from medmlx_core.upsample import deconv2x_ncdhw
+
+
+class ChannelLastGraph:
+    def __init__(self, weights: Mapping[str, Any], *, mx: Any) -> None:
+        self.w = weights
+        self.mx = mx
+
+    def conv(self, x: Any, name: str, *, padding: int = 0, stride: int = 1, groups: int = 1) -> Any:
+        w = self.w[f"{name}.weight"]
+        axes = (0, *range(2, w.ndim), 1)
+        operation = self.mx.conv3d if w.ndim == 5 else self.mx.conv2d
+        y = operation(x, w.transpose(axes), stride=stride, padding=padding, groups=groups)
+        bias = self.w.get(f"{name}.bias")
+        return y if bias is None else y + bias
+
+    def linear(self, x: Any, name: str) -> Any:
+        y = x @ self.w[f"{name}.weight"].T
+        bias = self.w.get(f"{name}.bias")
+        return y if bias is None else y + bias
+
+    def layer_norm(self, x: Any, name: str | None = None) -> Any:
+        weight = None if name is None else self.w[f"{name}.weight"]
+        bias = None if name is None else self.w[f"{name}.bias"]
+        return self.mx.fast.layer_norm(x, weight, bias, 1e-5)
+
+    def batch_norm(self, x: Any, name: str, *, eps: float = 1e-5) -> Any:
+        scale = self.w[f"{name}.weight"] * self.mx.rsqrt(self.w[f"{name}.running_var"] + eps)
+        return (x - self.w[f"{name}.running_mean"]) * scale + self.w[f"{name}.bias"]
+
+    def relu(self, x: Any) -> Any:
+        return self.mx.maximum(x, 0)
+
+    def swish(self, x: Any) -> Any:
+        return x * self.mx.sigmoid(x)
+
+    def instance_norm(self, x: Any) -> Any:
+        axes = tuple(range(1, x.ndim - 1))
+        mean = self.mx.mean(x, axis=axes, keepdims=True)
+        return (x - mean) * self.mx.rsqrt(self.mx.var(x, axis=axes, keepdims=True) + 1e-5)
+
+    def residual3d(self, x: Any, name: str) -> Any:
+        def activate(y: Any) -> Any:
+            return self.mx.where(y >= 0, y, y * 0.01)
+
+        y = activate(self.instance_norm(self.conv(x, f"{name}.conv1.conv", padding=1)))
+        y = self.instance_norm(self.conv(y, f"{name}.conv2.conv", padding=1))
+        if f"{name}.conv3.conv.weight" in self.w:
+            x = self.instance_norm(self.conv(x, f"{name}.conv3.conv"))
+        return activate(y + x)
+
+    def deconv3d(self, x: Any, name: str) -> Any:
+        result = deconv2x_ncdhw(
+            x.transpose(0, 4, 1, 2, 3), self.w[f"{name}.weight"], None, mx=self.mx
+        )
+        return result.transpose(0, 2, 3, 4, 1)
+
+    def bilinear2x(self, x: Any) -> Any:
+        """Source HoVer-Net uses align_corners=True at every 2x decoder stage."""
+        mx = self.mx
+        for axis in (1, 2):
+            size = x.shape[axis]
+            coordinate = mx.arange(size * 2, dtype=mx.float32) * ((size - 1) / (size * 2 - 1))
+            low = mx.floor(coordinate).astype(mx.int32)
+            high = mx.minimum(low + 1, size - 1)
+            fraction = coordinate - low.astype(mx.float32)
+            shape = [1] * x.ndim
+            shape[axis] = size * 2
+            fraction = fraction.reshape(shape)
+            x = mx.take(x, low, axis=axis) * (1 - fraction) + mx.take(x, high, axis=axis) * fraction
+        return x
+
+    def require_input(self, x: Any, shape: tuple[int, ...]) -> None:
+        if x.ndim != len(shape) + 1 or tuple(x.shape[1:]) != shape or x.shape[0] < 1:
+            raise ValueError(f"Expected Bx{'x'.join(map(str, shape))} input; got {x.shape}")
+        if x.dtype != self.mx.float32:
+            raise ValueError("MedMLX channel-last graphs require float32 inputs")

medmlx_core/checkpoints.py

@@ -0,0 +1,68 @@
+"""Host checkpoint deserialization shared by native model converters."""
+
+from __future__ import annotations
+
+from collections.abc import Mapping, Sequence
+from typing import cast
+
+import numpy as np
+from numpy.typing import NDArray
+
+from medmlx_core.conversion import load_torch_checkpoint
+from medmlx_core.errors import InvalidInputError
+
+HostArray = NDArray[np.generic]
+
+
+def mapping_from_pairs(
+    pairs: Sequence[tuple[str, HostArray]], *, what: str
+) -> dict[str, HostArray]:
+    """Build a tensor mapping or reject duplicate names."""
+
+    tensors: dict[str, HostArray] = {}
+    for name, array in pairs:
+        if name in tensors:
+            raise InvalidInputError(f"duplicate {what} parameter: {name}")
+        tensors[name] = array
+    return tensors
+
+
+def tensor_mapping_from_payload(payload: object, *, what: str) -> dict[str, HostArray]:
+    if not isinstance(payload, Mapping):
+        raise InvalidInputError(f"{what} checkpoint payload must be a mapping")
+    pairs: list[tuple[str, HostArray]] = []
+    mapping = cast(Mapping[object, object], payload)
+    for raw_name, value in mapping.items():
+        name = str(raw_name)
+        array = _maybe_array(value)
+        if array is None:
+            continue
+        pairs.append((name, array))
+    return mapping_from_pairs(pairs, what=what)
+
+
+def _maybe_array(value: object) -> HostArray | None:
+    if isinstance(value, np.ndarray):
+        return cast(HostArray, value)
+    if isinstance(value, (np.generic, int, float, bool, str)):
+        return None
+    detach = getattr(value, "detach", None)
+    tensor = detach() if callable(detach) else value
+    cpu = getattr(tensor, "cpu", None)
+    host = cpu() if callable(cpu) else tensor
+    numpy_fn = getattr(host, "numpy", None)
+    if not callable(numpy_fn):
+        return None
+    raw_array: object = numpy_fn()
+    if not isinstance(raw_array, np.ndarray):
+        raise InvalidInputError("tensor numpy() must return an ndarray")
+    return cast(HostArray, raw_array)
+
+
+__all__ = [
+    "HostArray",
+    "_maybe_array",
+    "load_torch_checkpoint",
+    "mapping_from_pairs",
+    "tensor_mapping_from_payload",
+]

medmlx_core/conversion.py

@@ -0,0 +1,31 @@
+"""Optional Torch checkpoint deserialization; install the conversion extra."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import cast
+
+from medmlx_core.errors import InvalidInputError, MissingDependencyError
+
+type RawCheckpoint = dict[object, object]
+
+
+def load_torch_checkpoint(path: Path, *, weights_only: bool = True) -> RawCheckpoint:
+    """Deserialize source weights on the host; requires Torch, without model execution."""
+
+    try:
+        import torch
+    except ImportError as exc:
+        raise MissingDependencyError(
+            "Checkpoint conversion requires torch to unpickle the source files",
+            extra="conversion",
+            hint="Install medmlx-core[conversion] and rerun the converter.",
+        ) from exc
+    payload: object = torch.load(path, map_location="cpu", weights_only=weights_only)
+    if not isinstance(payload, dict):
+        raise InvalidInputError(f"{path.name} is not a mapping checkpoint")
+    # Deserialization proves only a raw mapping; tensor_mapping_from_payload parses it.
+    return cast(RawCheckpoint, payload)
+
+
+__all__ = ["load_torch_checkpoint"]

medmlx_core/errors.py

@@ -0,0 +1,87 @@
+"""Shared MedMLX exceptions with builtin base classes."""
+
+from __future__ import annotations
+
+
+class MedmlxError(Exception):
+    """Base class for every error raised by the public MedMLX API."""
+
+    def __str__(self) -> str:
+        if not self.args:
+            return ""
+        if len(self.args) == 1:
+            return str(self.args[0])
+        return str(self.args)
+
+
+class MissingDependencyError(MedmlxError, ImportError):
+    """Raised when an optional model dependency/extra is not installed.
+
+    Args:
+        message: Human-readable description of the missing dependency.
+        extra: The pip extra that provides the dependency (e.g. ``"conversion"``),
+            or ``None`` when no single extra covers it.
+        hint: An actionable install/setup hint, e.g.
+            ``"Install medmlx-core[conversion]"``.
+
+    Attributes:
+        extra (str | None): The pip extra carrying the dependency.
+        hint (str | None): Suggested install/setup command.
+    """
+
+    def __init__(
+        self,
+        message: str,
+        *,
+        extra: str | None = None,
+        hint: str | None = None,
+    ) -> None:
+        super().__init__(message)
+        self.extra = extra
+        self.hint = hint
+
+
+class ModelExecutionError(MedmlxError, RuntimeError):
+    """Raised when a model runner fails during execution.
+
+    This signals a model/runtime failure, not a caller input error.
+    """
+
+
+class InvalidInputError(MedmlxError, ValueError):
+    """Raised when caller-supplied inputs are missing, malformed, or an unsupported combination."""
+
+
+class AssetNotReadyError(MedmlxError, FileNotFoundError):
+    """Raised when a model's local assets or checkpoints are missing or mismatched.
+
+    Args:
+        message: Human-readable description of the missing or incompatible asset.
+        reason: Short machine-friendly reason, e.g.
+            ``"missing weights/model.safetensors"``.
+        hint: An actionable setup hint, e.g. a model checkpoint conversion command.
+
+    Attributes:
+        reason (str | None): Why the asset is not ready.
+        hint (str | None): Suggested conversion or setup command.
+    """
+
+    def __init__(
+        self,
+        message: str,
+        *,
+        reason: str | None = None,
+        hint: str | None = None,
+    ) -> None:
+        super().__init__(message)
+        self.reason = reason
+        self.hint = hint
+
+
+__all__ = [
+    "AssetNotReadyError",
+    "InvalidInputError",
+    "MedmlxError",
+    "MissingDependencyError",
+    "ModelExecutionError",
+]

medmlx_core/layout.py

@@ -0,0 +1,70 @@
+"""NCDHW module layout and NDHWC remaps for MLX 3D conv/norm."""
+
+from __future__ import annotations
+
+from typing import Any
+
+LAYOUT_NCDHW = "maisi.layout.ncdhw"
+LAYOUT_TO_NDHWC = "maisi.layout.to_ndhwc"
+LAYOUT_TO_NCDHW = "maisi.layout.to_ncdhw"
+LAYOUT_CONV3D_W = "maisi.layout.conv3d_w"
+LAYOUT_CONV_TRANSPOSE3D_W = "maisi.layout.conv_transpose3d_w"
+LAYOUT_LINEAR_W = "maisi.layout.linear_w"
+LAYOUT_EMBED_W = "maisi.layout.embed_w"
+LAYOUT_GN_AFFINE = "maisi.layout.gn_affine"
+LAYOUT_VECTOR = "maisi.layout.vector"
+IDENTITY_WEIGHT_LAYOUTS = frozenset(
+    {LAYOUT_LINEAR_W, LAYOUT_EMBED_W, LAYOUT_GN_AFFINE, LAYOUT_VECTOR}
+)
+
+
+def require_ncdhw(array: Any, *, name: str) -> None:
+    """Raise if *array* is not a rank-5 NCDHW tensor."""
+
+    if int(array.ndim) != 5:
+        raise ValueError(f"{name} must be NCDHW rank-5; got ndim={array.ndim}")
+
+
+def to_ndhwc(array: Any, mx: Any) -> Any:
+    """NCDHW → NDHWC at a conv/norm call."""
+
+    return mx.transpose(array, (0, 2, 3, 4, 1))
+
+
+def to_ncdhw(array: Any, mx: Any) -> Any:
+    """NDHWC → NCDHW after a conv/norm call."""
+
+    return mx.transpose(array, (0, 4, 1, 2, 3))
+
+
+def conv3d_weight_to_mlx(weight: Any, mx: Any) -> Any:
+    """Torch conv3d weight [O, I, KD, KH, KW] → MLX [O, KD, KH, KW, I]."""
+
+    if int(weight.ndim) != 5:
+        raise ValueError(f"conv3d weight must be rank-5 [O,I,K]; got ndim={weight.ndim}")
+    return mx.transpose(weight, (0, 2, 3, 4, 1))
+
+
+def conv_transpose3d_weight_to_mlx(weight: Any, mx: Any) -> Any:
+    """Torch conv_transpose3d weight [I, O, KD, KH, KW] → MLX [O, KD, KH, KW, I]."""
+
+    if int(weight.ndim) != 5:
+        raise ValueError(f"conv_transpose3d weight must be rank-5 [I,O,K]; got ndim={weight.ndim}")
+    return mx.transpose(weight, (1, 2, 3, 4, 0))
+
+
+def tokens_from_ncdhw(array: Any, mx: Any) -> Any:
+    """NCDHW [B,C,D,H,W] → tokens [B, D*H*W, C]."""
+
+    require_ncdhw(array, name="attention input")
+    batch, channels, depth, height, width = (int(dim) for dim in array.shape)
+    flat = mx.reshape(array, (batch, channels, depth * height * width))
+    return mx.transpose(flat, (0, 2, 1))
+
+
+def tokens_to_ncdhw(tokens: Any, spatial: tuple[int, int, int, int, int], mx: Any) -> Any:
+    """Tokens [B, N, C] → NCDHW *spatial*."""
+
+    batch, channels, depth, height, width = spatial
+    ncdhw = mx.transpose(tokens, (0, 2, 1))
+    return mx.reshape(ncdhw, (batch, channels, depth, height, width))

medmlx_core/licenses/MONAI_LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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+
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+
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+      and distribution as defined by Sections 1 through 9 of this document.
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