Image Feature Extraction
Transformers
Safetensors
flexict
feature-extraction
medical-imaging
ct
vision
custom_code
Instructions to use ricklisz123/FlexiCT-3D with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use ricklisz123/FlexiCT-3D with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("image-feature-extraction", model="ricklisz123/FlexiCT-3D", trust_remote_code=True)# Load model directly from transformers import AutoModel model = AutoModel.from_pretrained("ricklisz123/FlexiCT-3D", trust_remote_code=True, dtype="auto") - Notebooks
- Google Colab
- Kaggle
| # Copyright (c) Meta Platforms, Inc. and affiliates. | |
| # | |
| # This software may be used and distributed in accordance with | |
| # the terms of the DINOv3 License Agreement. | |
| import math | |
| from typing import Literal | |
| import numpy as np | |
| import torch | |
| from torch import Tensor, nn | |
| # RoPE positional embedding with no mixing of coordinates (axial) and no learnable weights | |
| # Supports two parametrizations of the rope parameters: either using `base` or `min_period` and `max_period`. | |
| class RopePositionEmbedding(nn.Module): | |
| def __init__( | |
| self, | |
| embed_dim: int, | |
| *, | |
| num_heads: int, | |
| base: float | None = 100.0, | |
| min_period: float | None = None, | |
| max_period: float | None = None, | |
| normalize_coords: Literal["min", "max", "separate"] = "separate", | |
| shift_coords: float | None = None, | |
| jitter_coords: float | None = None, | |
| rescale_coords: float | None = None, | |
| dtype: torch.dtype | None = None, | |
| device: torch.device | None = None, | |
| ): | |
| super().__init__() | |
| assert embed_dim % (4 * num_heads) == 0 | |
| both_periods = min_period is not None and max_period is not None | |
| if (base is None and not both_periods) or (base is not None and both_periods): | |
| raise ValueError("Either `base` or `min_period`+`max_period` must be provided.") | |
| D_head = embed_dim // num_heads | |
| self.base = base | |
| self.min_period = min_period | |
| self.max_period = max_period | |
| self.D_head = D_head | |
| self.normalize_coords = normalize_coords | |
| self.shift_coords = shift_coords | |
| self.jitter_coords = jitter_coords | |
| self.rescale_coords = rescale_coords | |
| # Needs persistent=True because we do teacher.load_state_dict(student.state_dict()) to initialize the teacher | |
| self.dtype = dtype # Don't rely on self.periods.dtype | |
| self.register_buffer( | |
| "periods", | |
| torch.empty(D_head // 4, device=device, dtype=dtype), | |
| persistent=True, | |
| ) | |
| self._init_weights() | |
| def forward(self, *, H: int, W: int) -> tuple[Tensor, Tensor]: | |
| device = self.periods.device | |
| dtype = self.dtype | |
| dd = {"device": device, "dtype": dtype} | |
| # Prepare coords in range [-1, +1] | |
| if self.normalize_coords == "max": | |
| max_HW = max(H, W) | |
| coords_h = torch.arange(0.5, H, **dd) / max_HW # [H] | |
| coords_w = torch.arange(0.5, W, **dd) / max_HW # [W] | |
| elif self.normalize_coords == "min": | |
| min_HW = min(H, W) | |
| coords_h = torch.arange(0.5, H, **dd) / min_HW # [H] | |
| coords_w = torch.arange(0.5, W, **dd) / min_HW # [W] | |
| elif self.normalize_coords == "separate": | |
| coords_h = torch.arange(0.5, H, **dd) / H # [H] | |
| coords_w = torch.arange(0.5, W, **dd) / W # [W] | |
| else: | |
| raise ValueError(f"Unknown normalize_coords: {self.normalize_coords}") | |
| coords = torch.stack(torch.meshgrid(coords_h, coords_w, indexing="ij"), dim=-1) # [H, W, 2] | |
| coords = coords.flatten(0, 1) # [HW, 2] | |
| coords = 2.0 * coords - 1.0 # Shift range [0, 1] to [-1, +1] | |
| # Shift coords by adding a uniform value in [-shift, shift] | |
| if self.training and self.shift_coords is not None: | |
| shift_hw = torch.empty(2, **dd).uniform_(-self.shift_coords, self.shift_coords) | |
| coords += shift_hw[None, :] | |
| # Jitter coords by multiplying the range [-1, 1] by a log-uniform value in [1/jitter, jitter] | |
| if self.training and self.jitter_coords is not None: | |
| jitter_max = np.log(self.jitter_coords) | |
| jitter_min = -jitter_max | |
| jitter_hw = torch.empty(2, **dd).uniform_(jitter_min, jitter_max).exp() | |
| coords *= jitter_hw[None, :] | |
| # Rescale coords by multiplying the range [-1, 1] by a log-uniform value in [1/rescale, rescale] | |
| if self.training and self.rescale_coords is not None: | |
| rescale_max = np.log(self.rescale_coords) | |
| rescale_min = -rescale_max | |
| rescale_hw = torch.empty(1, **dd).uniform_(rescale_min, rescale_max).exp() | |
| coords *= rescale_hw | |
| # Prepare angles and sin/cos | |
| angles = 2 * math.pi * coords[:, :, None] / self.periods[None, None, :] # [HW, 2, D//4] | |
| angles = angles.flatten(1, 2) # [HW, D//2] | |
| angles = angles.tile(2) # [HW, D] | |
| cos = torch.cos(angles) # [HW, D] | |
| sin = torch.sin(angles) # [HW, D] | |
| return (sin, cos) # 2 * [HW, D] | |
| def _init_weights(self): | |
| device = self.periods.device | |
| dtype = self.dtype | |
| if self.base is not None: | |
| periods = self.base ** ( | |
| 2 * torch.arange(self.D_head // 4, device=device, dtype=dtype) / (self.D_head // 2) | |
| ) # [D//4] | |
| else: | |
| base = self.max_period / self.min_period | |
| exponents = torch.linspace(0, 1, self.D_head // 4, device=device, dtype=dtype) # [D//4] range [0, 1] | |
| periods = base**exponents # range [1, max_period / min_period] | |
| periods = periods / base # range [min_period / max_period, 1] | |
| periods = periods * self.max_period # range [min_period, max_period] | |
| self.periods.data = periods | |
| class RopePositionEmbedding3D(nn.Module): | |
| """ | |
| RoPE positional embedding for 3D grids with no mixing across axes (axial), | |
| and no learnable weights. | |
| Supports two parametrizations of the rope parameters: either using `base` | |
| or `min_period` + `max_period`. | |
| Returns (sin, cos) each shaped [D*H*W, D_head], suitable for applying to q/k. | |
| """ | |
| def __init__( | |
| self, | |
| embed_dim: int, | |
| *, | |
| num_heads: int, | |
| base: float | None = 100.0, | |
| min_period: float | None = None, | |
| max_period: float | None = None, | |
| normalize_coords: Literal["min", "max", "separate"] = "separate", | |
| shift_coords: float | None = None, | |
| jitter_coords: float | None = None, | |
| rescale_coords: float | None = None, | |
| dtype: torch.dtype | None = None, | |
| device: torch.device | None = None, | |
| ): | |
| super().__init__() | |
| # For 3 axes, per-axis rotary block is D_head//6 | |
| assert embed_dim % (6 * num_heads) == 0, \ | |
| "For 3D RoPE, embed_dim must be divisible by 6 * num_heads." | |
| both_periods = (min_period is not None) and (max_period is not None) | |
| if (base is None and not both_periods) or (base is not None and both_periods): | |
| raise ValueError("Either `base` or `min_period`+`max_period` must be provided.") | |
| D_head = embed_dim // num_heads | |
| self.base = base | |
| self.min_period = min_period | |
| self.max_period = max_period | |
| self.D_head = D_head | |
| self.normalize_coords = normalize_coords | |
| self.shift_coords = shift_coords | |
| self.jitter_coords = jitter_coords | |
| self.rescale_coords = rescale_coords | |
| # Keep a persistent buffer so teacher.load_state_dict(student.state_dict()) works. | |
| self.dtype = dtype # Don't rely on self.periods.dtype | |
| self.register_buffer( | |
| "periods", | |
| torch.empty(D_head // 6, device=device, dtype=dtype), | |
| persistent=True, | |
| ) | |
| self._init_weights() | |
| def _init_weights(self): | |
| device = self.periods.device | |
| dtype = self.dtype | |
| per_axis_block = self.D_head // 6 # 3 axes × per_axis_block = D_head//2 | |
| if self.base is not None: | |
| # Classic exponential spectrum | |
| periods = self.base ** ( | |
| 2 * torch.arange(per_axis_block, device=device, dtype=dtype) / (self.D_head // 2) | |
| ) # [per_axis_block] | |
| else: | |
| # Linearly spaced in log-period between min_period and max_period | |
| base = self.max_period / self.min_period | |
| exponents = torch.linspace(0, 1, per_axis_block, device=device, dtype=dtype) | |
| periods = base**exponents # [1, base] | |
| periods = periods / base # [1/base, 1] | |
| periods = periods * self.max_period # [min_period, max_period] | |
| self.periods.data = periods | |
| def forward(self, *, D: int, H: int, W: int) -> tuple[Tensor, Tensor]: | |
| """ | |
| Args: | |
| D, H, W: depth, height, width (integers) | |
| Returns: | |
| (sin, cos): two tensors of shape [D*H*W, D_head] | |
| """ | |
| device = self.periods.device | |
| dtype = self.dtype | |
| dd = {"device": device, "dtype": dtype} | |
| # --- Build normalized coords in [-1, +1] for each axis --- | |
| if self.normalize_coords == "max": | |
| m = max(D, H, W) | |
| coords_d = torch.arange(0.5, D, **dd) / m # [D] | |
| coords_h = torch.arange(0.5, H, **dd) / m # [H] | |
| coords_w = torch.arange(0.5, W, **dd) / m # [W] | |
| elif self.normalize_coords == "min": | |
| m = min(D, H, W) | |
| coords_d = torch.arange(0.5, D, **dd) / m | |
| coords_h = torch.arange(0.5, H, **dd) / m | |
| coords_w = torch.arange(0.5, W, **dd) / m | |
| elif self.normalize_coords == "separate": | |
| coords_d = torch.arange(0.5, D, **dd) / D | |
| coords_h = torch.arange(0.5, H, **dd) / H | |
| coords_w = torch.arange(0.5, W, **dd) / W | |
| else: | |
| raise ValueError(f"Unknown normalize_coords: {self.normalize_coords}") | |
| # Meshgrid in (D, H, W) order; last dim stacks (d, h, w) | |
| coords = torch.stack( | |
| torch.meshgrid(coords_d, coords_h, coords_w, indexing="ij"), | |
| dim=-1 | |
| ) # [D, H, W, 3] | |
| coords = coords.flatten(0, 2) # [DHW, 3] | |
| coords = 2.0 * coords - 1.0 # shift [0,1] -> [-1,1] | |
| # --- Optional data-aug on coords (train-time only) --- | |
| if self.training and self.shift_coords is not None: | |
| shift_dhw = torch.empty(3, **dd).uniform_(-self.shift_coords, self.shift_coords) | |
| coords = coords + shift_dhw[None, :] | |
| if self.training and self.jitter_coords is not None: | |
| jitter_max = np.log(self.jitter_coords) | |
| jitter_min = -jitter_max | |
| jitter_dhw = torch.empty(3, **dd).uniform_(jitter_min, jitter_max).exp() | |
| coords = coords * jitter_dhw[None, :] | |
| if self.training and self.rescale_coords is not None: | |
| rescale_max = np.log(self.rescale_coords) | |
| rescale_min = -rescale_max | |
| rescale = torch.empty(1, **dd).uniform_(rescale_min, rescale_max).exp() | |
| coords = coords * rescale | |
| # --- Build rotary angles (axial, no mixing) --- | |
| # periods: [P] where P = D_head//6 | |
| # coords: [N, 3], broadcast => [N, 3, P] | |
| angles = 2 * math.pi * coords[:, :, None] / self.periods[None, None, :] # [N, 3, P] | |
| angles = angles.flatten(1, 2) # [N, 3*P] == [N, D_head//2] | |
| angles = angles.tile(2) # [N, D_head] | |
| cos = torch.cos(angles) | |
| sin = torch.sin(angles) | |
| return (sin, cos) |