rpotter6298
512ebd13b2
- Introduced `protocol.py` for shared data models used in server/client communication, including request and response schemas for registration, job submission, and status updates. - Implemented `server.py` to manage a SQLite job queue and client registry, handling job polling, status updates, and job completion. - Created a cheat sheet for server usage, detailing commands for starting the server, submitting jobs, and monitoring clients. - Added several experiment configuration files for various training setups, including geometry vector injections and baseline ensembles.
238 lines
8.7 KiB
Python
238 lines
8.7 KiB
Python
"""geometry_tower — GeometrySegEncoder for v4.
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A CNN tower that takes a per-eye disc/cup *segmentation map* as input (rather
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than the raw fundus image) and contributes its pooled embedding to fusion.
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Seg maps are produced by an underlying loader (GT contour rasterisation or
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UNet inference) during early_pass, then cached per fold.
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UNet fine-tuning lives in early_pass too — the loader's `finetune(train_samples)`
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call uses only the training split, then precompute() runs inference on all
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fold samples (train + val + test).
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Config example:
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{
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"name": "geom",
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"module": "v4.classes.towers.geometry_tower",
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"class": "GeometrySegEncoder",
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"data_source": "image",
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"args": {
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"backbone": "resnet18",
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"channels": 3,
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"target_size": 224,
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"augment": true,
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"seg_source": "gt",
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"contour_dir": "Papila/ExpertsSegmentations/Contours"
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}
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}
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"""
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from __future__ import annotations
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import math
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import sys
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from pathlib import Path
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from typing import Any
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import numpy as np
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import torch
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from torch import nn
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from torchvision import models
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_REPO_ROOT = Path(__file__).resolve().parents[3]
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if str(_REPO_ROOT) not in sys.path:
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sys.path.insert(0, str(_REPO_ROOT))
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from v4.classes.accessory.backbones import build_backbone
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from v4.classes.towerbase import TowerBase
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class GeometrySegEncoder(TowerBase):
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"""CNN tower over disc/cup segmentation maps.
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image_data : ImageDataView — provides get_image_path(*ids) and side_map.
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Must implement build_seg_map_loader(source, **kwargs).
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backbone : backbone key (see accessory/backbones.py)
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channels : 1 (label map in [0,1]) or 3 (one-hot bg/rim/cup)
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target_size : CNN input spatial size (cached arrays already at this size)
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augment : random flip + 90° rotation at training time
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freeze_ratio : fraction of early backbone blocks to freeze in [0, 1]
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seg_source : passed to image_data.build_seg_map_loader (e.g. "gt", "unet")
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**seg_kwargs : forwarded to build_seg_map_loader
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"""
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def __init__(
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self,
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image_data,
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backbone: str = "resnet18",
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channels: int = 3,
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target_size: int = 224,
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augment: bool = True,
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freeze_ratio: float = 0.0,
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seg_source: str = "gt",
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**seg_kwargs: Any,
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):
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super().__init__()
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self.image_data = image_data
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self._channels = channels
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self._target_size = target_size
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self._augment = augment
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if not hasattr(image_data, "build_seg_map_loader"):
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raise TypeError(
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f"GeometrySegEncoder requires image_data to implement "
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f"build_seg_map_loader(), but {type(image_data).__name__} does not."
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)
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loader_kwargs = {
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"channels": channels,
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"target_size": target_size,
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**seg_kwargs,
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}
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self._loader = image_data.build_seg_map_loader(seg_source, **loader_kwargs)
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self._seg_cache: dict = {}
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self._seg_source = seg_source
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self.backbone, self._base_dim, self._blocks = build_backbone(backbone, freeze_ratio)
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if channels != 3:
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self._adapt_first_conv(channels)
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print(
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f"[GeometrySegEncoder] backbone={backbone} channels={channels} "
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f"target_size={target_size} seg_source={seg_source}",
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flush=True,
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)
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# ── TowerBase interface ──────────────────────────────────────────────────
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@property
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def out_dim(self) -> int:
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return self._base_dim
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@property
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def _side_map(self) -> dict[str, str]:
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return self.image_data.side_map
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def _get(self, *ids) -> torch.Tensor:
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key = tuple(ids)
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arr = self._seg_cache.get(key)
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if arr is None:
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arr = np.zeros(
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(self._channels, self._target_size, self._target_size),
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dtype=np.float32,
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)
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if self.training and self._augment:
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arr = self._augment_array(arr)
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return torch.from_numpy(np.ascontiguousarray(arr))
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# ── EPC early_pass ───────────────────────────────────────────────────────
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def early_pass(self, context) -> None:
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data = context.require("data")
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split = context.require("split")
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train_samples = self._collect_samples(split.train, data)
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all_samples = self._collect_samples(split.train, data)
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all_samples += self._collect_samples(split.val, data)
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if split.test is not None:
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all_samples += self._collect_samples(split.test, data)
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# Reset per-fold state if loader supports it (UNet only).
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if hasattr(self._loader, "reset_cache"):
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self._loader.reset_cache()
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if hasattr(self._loader, "reset_weights"):
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self._loader.reset_weights()
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if hasattr(self._loader, "finetune"):
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self._loader.finetune(train_samples)
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self._loader.precompute(all_samples)
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self._seg_cache = self._loader.all_seg_maps()
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print(
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f"[GeometrySegEncoder] cached {len(self._seg_cache)} seg maps for fold",
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flush=True,
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)
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# ── nn.Module forward ────────────────────────────────────────────────────
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def forward(self, x: torch.Tensor) -> torch.Tensor:
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y = self.backbone(x)
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if y.dim() > 2:
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y = y.flatten(1)
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return y
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# ── Utilities ────────────────────────────────────────────────────────────
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def set_freeze_ratio(self, ratio: float) -> None:
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r = max(0.0, min(1.0, float(ratio)))
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n_freeze = int(math.floor(len(self._blocks) * r))
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for b in self._blocks:
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for p in b.parameters():
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p.requires_grad = True
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for b in self._blocks[:n_freeze]:
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for p in b.parameters():
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p.requires_grad = False
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# ── Internals ────────────────────────────────────────────────────────────
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def _collect_samples(self, df, data) -> list:
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"""Build (pid, eye, image_path) tuples from a split DataFrame."""
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if df is None or len(df) == 0:
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return []
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pc = data.patient_col
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out = []
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for _, row in df.iterrows():
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pid = int(row[pc])
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eye = str(row.get("eyeID", "OD"))
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out.append((pid, eye, data.image.get_image_path(pid, eye)))
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return out
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@staticmethod
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def _augment_array(arr: np.ndarray) -> np.ndarray:
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"""Random flip + 90° rotation on a (C, H, W) seg-map array."""
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if np.random.rand() < 0.5:
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arr = arr[:, :, ::-1]
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if np.random.rand() < 0.5:
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arr = arr[:, ::-1, :]
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k = int(np.random.randint(0, 4))
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if k:
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arr = np.rot90(arr, k=k, axes=(1, 2))
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return arr
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def _adapt_first_conv(self, in_channels: int) -> None:
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"""Replace the first Conv2d to accept a non-3-channel input.
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Pretrained weights are averaged across the original input channels and
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broadcast across the new ones.
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"""
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first = self._find_first_conv(self.backbone)
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new = nn.Conv2d(
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in_channels,
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first.out_channels,
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kernel_size=first.kernel_size,
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stride=first.stride,
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padding=first.padding,
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bias=first.bias is not None,
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)
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with torch.no_grad():
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new.weight.copy_(
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first.weight.mean(dim=1, keepdim=True).expand_as(new.weight)
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)
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if first.bias is not None:
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new.bias.copy_(first.bias)
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self._replace_first_conv(self.backbone, new)
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@staticmethod
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def _find_first_conv(module: nn.Module) -> nn.Conv2d:
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for m in module.modules():
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if isinstance(m, nn.Conv2d):
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return m
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raise RuntimeError("No Conv2d found in backbone")
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@classmethod
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def _replace_first_conv(cls, module: nn.Module, new_conv: nn.Conv2d) -> bool:
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for name, child in module.named_children():
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if isinstance(child, nn.Conv2d):
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setattr(module, name, new_conv)
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return True
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if cls._replace_first_conv(child, new_conv):
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return True
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return False
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