mipcandy 1.0.0__tar.gz

mipcandy-1.0.0/.gitignore

@@ -0,0 +1,7 @@
+.idea
+__pycache__
+main.py
+build
+*.egg-info
+dist
+secrets.yml

mipcandy-1.0.0/LICENSE

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mipcandy-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mipcandy
+Version: 1.0.0
+Summary: A Candy for Medical Image Processing
+Project-URL: Homepage, https://mipcandy.projectneura.org
+Project-URL: Documentation, https://mipcandy-docs.projectneura.org
+Project-URL: Repository, https://github.com/ProjectNeura/MIPCandy
+Author-email: Project Neura <central@projectneura.org>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: ptflops
+Requires-Dist: requests
+Requires-Dist: rich
+Requires-Dist: simpleitk
+Requires-Dist: torch
+Provides-Extra: standard
+Requires-Dist: pyvista; extra == 'standard'
+Description-Content-Type: text/markdown
+
+# MIP Candy: A Candy for Medical Image Processing
+
+![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/ProjectNeura/MIPCandy)
+![PyPI](https://img.shields.io/pypi/v/mip_candy)
+![GitHub Release](https://img.shields.io/github/v/release/ProjectNeura/MIPCandy)
+![GitHub Release Date - Published_At](https://img.shields.io/github/release-date/ProjectNeura/MIPCandy)
+
+MIP Candy is Project Neura's next-generation infrastructure framework for medical image processing. It integrates a
+handful number of common network architectures with their corresponding training, inference, and evaluation pipelines
+that are out-of-the-box ready to use. Additionally, it also provides adapters to popular frontend dashboards such as
+Notion, WandB, and TensorBoard.
+
+:link: [Docs](https://mipcandy-docs.projectneura.org)
+
+## Installation
+
+Note that MIP Candy requires **Python >= 3.12**.
+
+```shell
+pip install "mipcandy[standard]"
+```

mipcandy-1.0.0/README.md

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+# MIP Candy: A Candy for Medical Image Processing
+
+![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/ProjectNeura/MIPCandy)
+![PyPI](https://img.shields.io/pypi/v/mip_candy)
+![GitHub Release](https://img.shields.io/github/v/release/ProjectNeura/MIPCandy)
+![GitHub Release Date - Published_At](https://img.shields.io/github/release-date/ProjectNeura/MIPCandy)
+
+MIP Candy is Project Neura's next-generation infrastructure framework for medical image processing. It integrates a
+handful number of common network architectures with their corresponding training, inference, and evaluation pipelines
+that are out-of-the-box ready to use. Additionally, it also provides adapters to popular frontend dashboards such as
+Notion, WandB, and TensorBoard.
+
+:link: [Docs](https://mipcandy-docs.projectneura.org)
+
+## Installation
+
+Note that MIP Candy requires **Python >= 3.12**.
+
+```shell
+pip install "mipcandy[standard]"
+```

mipcandy-1.0.0/mipcandy/__init__.py

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+from mipcandy.common import *
+from mipcandy.data import *
+from mipcandy.evaluation import EvalCase, EvalResult, Evaluator
+from mipcandy.frontend import *
+from mipcandy.inference import parse_predictant, Predictor
+from mipcandy.layer import batch_int_multiply, batch_int_divide, LayerT, HasDevice, WithPaddingModule
+from mipcandy.metrics import do_reduction, dice_similarity_coefficient_binary, \
+    dice_similarity_coefficient_multiclass, soft_dice_coefficient, accuracy_binary, accuracy_multiclass, \
+    precision_binary, precision_multiclass, recall_binary, recall_multiclass, iou_binary, iou_multiclass
+from mipcandy.preset import *
+from mipcandy.sanity_check import num_trainable_params, sanity_check
+from mipcandy.training import TrainerToolbox, Trainer, SWMetadata, SlidingTrainer
+from mipcandy.types import Secret, Secrets, Params, Transform, SupportedPredictant, Colormap

mipcandy-1.0.0/mipcandy/common/__init__.py

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+from mipcandy.common.module import *
+from mipcandy.common.optim import *

mipcandy-1.0.0/mipcandy/common/module/__init__.py

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+from mipcandy.common.module.conv import ConvBlock2d, ConvBlock3d, WSConv2d, WSConv3d
+from mipcandy.common.module.preprocess import Pad2d, Pad3d, Restore2d, Restore3d, Normalize, ColorizeLabel

mipcandy-1.0.0/mipcandy/common/module/conv.py

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+from typing import override
+
+import torch
+from torch import nn
+
+from mipcandy.layer import LayerT
+
+
+class AbstractConvBlock(nn.Module):
+    def __init__(self, in_ch: int, out_ch: int, kernel_size: int, *, stride: int = 1, padding: int = 0,
+                 dilation: int = 1, groups: int = 1, bias: bool = True, padding_mode: str = "zeros",
+                 conv: LayerT = ..., norm: LayerT = ..., act: LayerT = ...) -> None:
+        super().__init__()
+        self.conv: nn.Module = conv.assemble(in_ch, out_ch, kernel_size, stride, padding, dilation, groups, bias,
+                                             padding_mode)
+        self.norm: nn.Module = norm.assemble(in_ch=out_ch)
+        self.act: nn.Module = act.assemble()
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        return self.act(self.norm(self.conv(x)))
+
+
+def _conv_block(default_conv: LayerT, default_norm: LayerT, default_act: LayerT) -> type[AbstractConvBlock]:
+    class ConvBlock(AbstractConvBlock):
+        def __init__(self, *args, **kwargs) -> None:
+            if "conv" not in kwargs:
+                kwargs["conv"] = default_conv
+            if "norm" not in kwargs:
+                kwargs["norm"] = default_norm
+            if "act" not in kwargs:
+                kwargs["act"] = default_act
+            super().__init__(*args, **kwargs)
+
+    return ConvBlock
+
+
+ConvBlock2d: type[AbstractConvBlock] = _conv_block(
+    LayerT(nn.Conv2d), LayerT(nn.BatchNorm2d, num_features="in_ch"), LayerT(nn.ReLU, inplace=True)
+)
+
+ConvBlock3d: type[AbstractConvBlock] = _conv_block(
+    LayerT(nn.Conv3d), LayerT(nn.BatchNorm3d, num_features="in_ch"), LayerT(nn.ReLU, inplace=True)
+)
+
+
+class WSConv2d(nn.Conv2d):
+    @override
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        w = self.weight
+        w = (w - w.mean(dim=(1, 2, 3), keepdim=True)) / (w.std(dim=(1, 2, 3), keepdim=True) + 1e-5)
+        return nn.functional.conv2d(x, w, self.bias, self.stride, self.padding, self.dilation, self.groups)
+
+
+class WSConv3d(nn.Conv3d):
+    @override
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        w = self.weight
+        w = (w - w.mean(dim=(1, 2, 3, 4), keepdim=True)) / (w.std(dim=(1, 2, 3, 4), keepdim=True) + 1e-5)
+        return nn.functional.conv3d(x, w, self.bias, self.stride, self.padding, self.dilation, self.groups)

mipcandy-1.0.0/mipcandy/common/module/preprocess.py

@@ -0,0 +1,179 @@
+from math import ceil
+from typing import Literal
+
+import torch
+from torch import nn
+
+from mipcandy.types import Colormap
+
+
+class Pad(nn.Module):
+    def __init__(self, *, value: int = 0, mode: str = "constant", batch: bool = True) -> None:
+        super().__init__()
+        self._value: int = value
+        self._mode: str = mode
+        self.batch: bool = batch
+        self._paddings: tuple[int, int, int, int, int, int] | tuple[int, int, int, int] | None = None
+        self.requires_grad_(False)
+
+    @staticmethod
+    def _c_t(size: int, min_factor: int) -> int:
+        """
+        Compute target on a single dimension
+        """
+        return ceil(size / min_factor) * min_factor
+
+    @staticmethod
+    def _c_p(size: int, min_factor: int) -> tuple[int, int]:
+        """
+        Compute padding on a single dimension
+        """
+        excess = Pad._c_t(size, min_factor) - size
+        before = excess // 2
+        return before, excess - before
+
+
+class Pad2d(Pad):
+    def __init__(self, min_factor: int | tuple[int, int], *, value: int = 0, mode: str = "constant",
+                 batch: bool = True) -> None:
+        super().__init__(value=value, mode=mode, batch=batch)
+        self._min_factor: tuple[int, int] = (min_factor,) * 2 if isinstance(min_factor, int) else min_factor
+
+    def paddings(self) -> tuple[int, int, int, int] | None:
+        return self._paddings
+
+    def padded_shape(self, in_shape: tuple[int, int, ...]) -> tuple[int, int, ...]:
+        return *in_shape[:-2], Pad._c_t(in_shape[-2], self._min_factor[0]), Pad._c_t(in_shape[-1], self._min_factor[1])
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        if self.batch:
+            _, _, h, w = x.shape
+            suffix = (0,) * 4
+        else:
+            _, h, w = x.shape
+            suffix = (0,) * 2
+        self._paddings = Pad._c_p(h, self._min_factor[0]) + Pad._c_p(w, self._min_factor[1])
+        return nn.functional.pad(x, self._paddings[::-1] + suffix, self._mode, self._value)
+
+
+class Pad3d(Pad):
+    def __init__(self, min_factor: int | tuple[int, int, int], *, value: int = 0, mode: str = "constant",
+                 batch: bool = True) -> None:
+        super().__init__(value=value, mode=mode, batch=batch)
+        self._min_factor: tuple[int, int, int] = (min_factor,) * 3 if isinstance(min_factor, int) else min_factor
+
+    def paddings(self) -> tuple[int, int, int, int, int, int] | None:
+        return self._paddings
+
+    def padded_shape(self, in_shape: tuple[int, int, int, ...]) -> tuple[int, int, int, ...]:
+        return (*in_shape[:-3], Pad._c_t(in_shape[-3], self._min_factor[0]), Pad._c_t(
+            in_shape[-2], self._min_factor[1]), Pad._c_t(in_shape[-1], self._min_factor[2]))
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        if self.batch:
+            _, _, d, h, w = x.shape
+            suffix = (0,) * 4
+        else:
+            _, d, h, w = x.shape
+            suffix = (0,) * 2
+        self._paddings = Pad._c_p(d, self._min_factor[2]) + Pad._c_p(h, self._min_factor[0]) + Pad._c_p(
+            w, self._min_factor[1])
+        return nn.functional.pad(x, self._paddings[::-1] + suffix, self._mode, self._value)
+
+
+class Restore2d(nn.Module):
+    def __init__(self, conjugate_padding: Pad2d) -> None:
+        super().__init__()
+        self.conjugate_padding: Pad2d = conjugate_padding
+        self.requires_grad_(False)
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        paddings = self.conjugate_padding.paddings()
+        if not paddings:
+            raise UserWarning("Paddings seem to be unset, did you forget to pad before restoring?")
+        pad_h0, pad_h1, pad_w0, pad_w1 = paddings
+        if self.conjugate_padding.batch:
+            _, _, h, w = x.shape
+            return x[:, :, pad_h0: h - pad_h1, pad_w0: w - pad_w1]
+        _, h, w = x.shape
+        return x[:, pad_h0: h - pad_h1, pad_w0: w - pad_w1]
+
+
+class Restore3d(nn.Module):
+    def __init__(self, conjugate_padding: Pad3d) -> None:
+        super().__init__()
+        self.conjugate_padding: Pad3d = conjugate_padding
+        self.requires_grad_(False)
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        paddings = self.conjugate_padding.paddings()
+        if not paddings:
+            raise UserWarning("Paddings seem to be unset, did you forget to pad before restoring?")
+        pad_h0, pad_h1, pad_w0, pad_w1, pad_d0, pad_d1 = paddings
+        if self.conjugate_padding.batch:
+            _, _, d, h, w = x.shape
+            return x[:, :, pad_d0: d - pad_d1, pad_h0: h - pad_h1, pad_w0: w - pad_w1]
+        _, d, h, w = x.shape
+        return x[:, pad_d0: d - pad_d1, pad_h0: h - pad_h1, pad_w0: w - pad_w1]
+
+
+class Normalize(nn.Module):
+    def __init__(self, *, domain: tuple[float | None, float | None] = (0, None), strict: bool = False,
+                 method: Literal["linear", "intercept", "cut"] = "linear") -> None:
+        super().__init__()
+        self._domain: tuple[float | None, float | None] = domain
+        self._strict: bool = strict
+        self._method: Literal["linear", "intercept", "cut"] = method
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        left, right = self._domain
+        if left is None and right is None:
+            return x
+        r_l, r_r = x.min(), x.max()
+        match self._method:
+            case "linear":
+                if left is None or (left < r_l and not self._strict):
+                    left = r_l
+                if right is None or (right > r_r and not self._strict):
+                    right = r_r
+                numerator = right - left
+                if numerator == 0:
+                    numerator = 1
+                denominator = r_r - r_l
+                if denominator == 0:
+                    denominator = 1
+                return (x - r_l) * numerator / denominator + left
+            case "intercept":
+                if left is not None and right is None:
+                    return x - r_l + left if r_l < left or self._strict else x
+                elif left is None and right is not None:
+                    return x - r_r + right if r_r > right or self._strict else x
+                else:
+                    raise ValueError("Cannot use intercept normalization when both ends are fixed")
+            case "cut":
+                if self._strict:
+                    raise ValueError("Method \"cut\" cannot be strict")
+                if left is not None:
+                    x[x < left] = left
+                if right is not None:
+                    x[x > right] = right
+                return x
+
+
+class ColorizeLabel(nn.Module):
+    def __init__(self, *, colormap: Colormap | None = None) -> None:
+        super().__init__()
+        if not colormap:
+            colormap = []
+            for r in range(8):
+                for g in range(8):
+                    for b in range(32):
+                        colormap.append([r * 32, g * 32, 255 - b * 32])
+        self._colormap: torch.Tensor = torch.tensor(colormap)
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        cmap = self._colormap.to(x.device)
+        return (
+            torch.cat([cmap[(x > 0).int()].permute(2, 0, 1), x.unsqueeze(0)]) if 0 <= x.min() < x.max() <= 1
+            else cmap[x.int()].permute(2, 0, 1)
+        )

mipcandy-1.0.0/mipcandy/common/optim/__init__.py

@@ -0,0 +1,2 @@
+from mipcandy.common.optim.loss import FocalBCEWithLogits, DiceBCELossWithLogits
+from mipcandy.common.optim.lr_scheduler import AbsoluteLinearLR

mipcandy-1.0.0/mipcandy/common/optim/loss.py

@@ -0,0 +1,41 @@
+from typing import Literal
+
+import torch
+from torch import nn
+
+from mipcandy.metrics import do_reduction, soft_dice_coefficient
+
+
+class FocalBCEWithLogits(nn.Module):
+    def __init__(self, alpha: float, gamma: float, *, reduction: Literal["mean", "sum", "none"] = "mean") -> None:
+        super().__init__()
+        self.alpha: float = alpha
+        self.gamma: float = gamma
+        self.reduction: Literal["mean", "sum", "none"] = reduction
+
+    def forward(self, logits: torch.Tensor, targets: torch.Tensor) -> torch.Tensor:
+        bce = nn.functional.binary_cross_entropy_with_logits(logits, targets, reduction="none")
+        p = torch.sigmoid(logits)
+        p_t = torch.where(targets.bool(), p, 1 - p)
+        alpha_t = torch.where(targets.bool(), torch.as_tensor(self.alpha, device=logits.device), torch.as_tensor(
+            1 - self.alpha, device=logits.device))
+        loss = alpha_t * (1 - p_t).pow(self.gamma) * bce
+        return do_reduction(loss, self.reduction)
+
+
+class DiceBCELossWithLogits(nn.Module):
+    def __init__(self, num_classes: int, *, lambda_bce: float = .5, lambda_soft_dice: float = 1,
+                 smooth: float = 1e-5) -> None:
+        super().__init__()
+        self.num_classes: int = num_classes
+        self.lambda_bce: float = lambda_bce
+        self.lambda_soft_dice: float = lambda_soft_dice
+        self.smooth: float = smooth
+
+    def forward(self, masks: torch.Tensor, labels: torch.Tensor) -> tuple[torch.Tensor, dict[str, float]]:
+        labels = labels.float()
+        bce = nn.functional.binary_cross_entropy_with_logits(masks, labels)
+        masks = masks.sigmoid()
+        soft_dice = soft_dice_coefficient(masks, labels, smooth=self.smooth)
+        c = self.lambda_bce * bce + self.lambda_soft_dice * (1 - soft_dice)
+        return c, {"soft dice": soft_dice.item(), "bce loss": bce.item()}

mipcandy-1.0.0/mipcandy/common/optim/lr_scheduler.py

@@ -0,0 +1,34 @@
+from typing import override
+
+from torch import optim
+
+
+class AbsoluteLinearLR(optim.lr_scheduler.LRScheduler):
+    """
+    lr = kx + b
+    """
+    def __init__(self, optimizer: optim.Optimizer, k: float, b: float, *, min_lr: float = 1e-6,
+                 restart: bool = False, last_epoch: int = -1) -> None:
+        self._k: float = k
+        self._b: float = b
+        if min_lr < 0:
+            raise ValueError(f"`min_lr` must be positive, but got {min_lr}")
+        self._min_lr: float = min_lr
+        self._restart: bool = restart
+        self._restart_step: int = 0
+        super().__init__(optimizer, last_epoch)
+
+    def _interp(self, step: int) -> float:
+        step -= self._restart_step
+        r = self._k * step + self._b
+        if r < self._min_lr:
+            if self._restart:
+                self._restart_step = step
+                return self._interp(step)
+            return self._min_lr
+        return r
+
+    @override
+    def get_lr(self) -> list[float]:
+        target = self._interp(self.last_epoch)
+        return [target for _ in self.optimizer.param_groups]

mipcandy-1.0.0/mipcandy/data/__init__.py

@@ -0,0 +1,6 @@
+from mipcandy.data.convertion import convert_ids_to_logits, convert_logits_to_ids
+from mipcandy.data.dataset import Loader, UnsupervisedDataset, SupervisedDataset, DatasetFromMemory, MergedDataset, \
+    NNUNetDataset, BinarizedDataset
+from mipcandy.data.geometric import ensure_num_dimensions, orthographic_views, aggregate_orthographic_views
+from mipcandy.data.io import resample_to_isotropic, load_image, save_image
+from mipcandy.data.visualization import visualize2d, visualize3d, overlay

mipcandy-1.0.0/mipcandy/data/convertion.py

@@ -0,0 +1,20 @@
+from typing import Literal
+
+import torch
+from torch import nn
+
+
+def convert_ids_to_logits(ids: torch.Tensor, d: Literal[1, 2, 3], num_classes: int) -> torch.Tensor:
+    if ids.dtype != torch.int or ids.min() < 0:
+        raise TypeError("`ids` should be positive integers")
+    d += 1
+    if ids.ndim != d:
+        if ids.ndim == d + 1 and ids.shape[1] == 1:
+            ids = ids.squeeze(1)
+        else:
+            raise ValueError(f"`ids` should be {d} dimensional or {d + 1} dimensional with single channel")
+    return nn.functional.one_hot(ids.long(), num_classes).movedim(-1, 1).float()
+
+
+def convert_logits_to_ids(logits: torch.Tensor, *, channel_dim: int = 1) -> torch.Tensor:
+    return logits.max(channel_dim).indices.int()