--- a +++ b/clinical_ts/xresnet1d.py @@ -0,0 +1,206 @@ +# AUTOGENERATED! DO NOT EDIT! File to edit: nbs/13_xresnet1d.ipynb (unless otherwise specified). + +__all__ = ['delegates', 'store_attr', 'init_default', 'BatchNorm', 'NormType', 'ConvLayer', 'AdaptiveAvgPool', + 'MaxPool', 'AvgPool', 'ResBlock', 'init_cnn', 'XResNet1d', 'xresnet1d18', 'xresnet1d34', 'xresnet1d50', + 'xresnet1d101', 'xresnet1d152', 'xresnet1d18_deep', 'xresnet1d34_deep', 'xresnet1d50_deep', + 'xresnet1d18_deeper', 'xresnet1d34_deeper', 'xresnet1d50_deeper'] + +# Cell +import torch +import torch.nn as nn +import torch.nn.functional as F + +from .basic_conv1d import create_head1d, Flatten + +from enum import Enum +import re + +# Cell +import inspect + +def delegates(to=None, keep=False): + "Decorator: replace `**kwargs` in signature with params from `to`" + def _f(f): + if to is None: to_f,from_f = f.__base__.__init__,f.__init__ + else: to_f,from_f = to,f + sig = inspect.signature(from_f) + sigd = dict(sig.parameters) + k = sigd.pop('kwargs') + s2 = {k:v for k,v in inspect.signature(to_f).parameters.items() + if v.default != inspect.Parameter.empty and k not in sigd} + sigd.update(s2) + if keep: sigd['kwargs'] = k + from_f.__signature__ = sig.replace(parameters=sigd.values()) + return f + return _f + +def store_attr(self, nms): + "Store params named in comma-separated `nms` from calling context into attrs in `self`" + mod = inspect.currentframe().f_back.f_locals + for n in re.split(', *', nms): setattr(self,n,mod[n]) + +# Cell +NormType = Enum('NormType', 'Batch BatchZero Weight Spectral Instance InstanceZero') + +def _conv_func(ndim=2, transpose=False): + "Return the proper conv `ndim` function, potentially `transposed`." + assert 1 <= ndim <=3 + return getattr(nn, f'Conv{"Transpose" if transpose else ""}{ndim}d') + +def init_default(m, func=nn.init.kaiming_normal_): + "Initialize `m` weights with `func` and set `bias` to 0." + if func and hasattr(m, 'weight'): func(m.weight) + with torch.no_grad(): + if getattr(m, 'bias', None) is not None: m.bias.fill_(0.) + return m + +def _get_norm(prefix, nf, ndim=2, zero=False, **kwargs): + "Norm layer with `nf` features and `ndim` initialized depending on `norm_type`." + assert 1 <= ndim <= 3 + bn = getattr(nn, f"{prefix}{ndim}d")(nf, **kwargs) + if bn.affine: + bn.bias.data.fill_(1e-3) + bn.weight.data.fill_(0. if zero else 1.) + return bn + +def BatchNorm(nf, ndim=2, norm_type=NormType.Batch, **kwargs): + "BatchNorm layer with `nf` features and `ndim` initialized depending on `norm_type`." + return _get_norm('BatchNorm', nf, ndim, zero=norm_type==NormType.BatchZero, **kwargs) + +# Cell +class ConvLayer(nn.Sequential): + "Create a sequence of convolutional (`ni` to `nf`), ReLU (if `use_activ`) and `norm_type` layers." + def __init__(self, ni, nf, ks=3, stride=1, padding=None, bias=None, ndim=2, norm_type=NormType.Batch, bn_1st=True, + act_cls=nn.ReLU, transpose=False, init=nn.init.kaiming_normal_, xtra=None, **kwargs): + if padding is None: padding = ((ks-1)//2 if not transpose else 0) + bn = norm_type in (NormType.Batch, NormType.BatchZero) + inn = norm_type in (NormType.Instance, NormType.InstanceZero) + if bias is None: bias = not (bn or inn) + conv_func = _conv_func(ndim, transpose=transpose) + conv = init_default(conv_func(ni, nf, kernel_size=ks, bias=bias, stride=stride, padding=padding, **kwargs), init) + if norm_type==NormType.Weight: conv = weight_norm(conv) + elif norm_type==NormType.Spectral: conv = spectral_norm(conv) + layers = [conv] + act_bn = [] + if act_cls is not None: act_bn.append(act_cls()) + if bn: act_bn.append(BatchNorm(nf, norm_type=norm_type, ndim=ndim)) + if inn: act_bn.append(InstanceNorm(nf, norm_type=norm_type, ndim=ndim)) + if bn_1st: act_bn.reverse() + layers += act_bn + if xtra: layers.append(xtra) + super().__init__(*layers) + +# Cell +def AdaptiveAvgPool(sz=1, ndim=2): + "nn.AdaptiveAvgPool layer for `ndim`" + assert 1 <= ndim <= 3 + return getattr(nn, f"AdaptiveAvgPool{ndim}d")(sz) + +def MaxPool(ks=2, stride=None, padding=0, ndim=2, ceil_mode=False): + "nn.MaxPool layer for `ndim`" + assert 1 <= ndim <= 3 + return getattr(nn, f"MaxPool{ndim}d")(ks, stride=stride, padding=padding) + +def AvgPool(ks=2, stride=None, padding=0, ndim=2, ceil_mode=False): + "nn.AvgPool layer for `ndim`" + assert 1 <= ndim <= 3 + return getattr(nn, f"AvgPool{ndim}d")(ks, stride=stride, padding=padding, ceil_mode=ceil_mode) + +# Cell +class ResBlock(nn.Module): + "Resnet block from `ni` to `nh` with `stride`" + @delegates(ConvLayer.__init__) + def __init__(self, expansion, ni, nf, stride=1, kernel_size=3, groups=1, reduction=None, nh1=None, nh2=None, dw=False, g2=1, + sa=False, sym=False, norm_type=NormType.Batch, act_cls=nn.ReLU, ndim=2, + pool=AvgPool, pool_first=True, **kwargs): + super().__init__() + norm2 = (NormType.BatchZero if norm_type==NormType.Batch else + NormType.InstanceZero if norm_type==NormType.Instance else norm_type) + if nh2 is None: nh2 = nf + if nh1 is None: nh1 = nh2 + nf,ni = nf*expansion,ni*expansion + k0 = dict(norm_type=norm_type, act_cls=act_cls, ndim=ndim, **kwargs) + k1 = dict(norm_type=norm2, act_cls=None, ndim=ndim, **kwargs) + layers = [ConvLayer(ni, nh2, kernel_size, stride=stride, groups=ni if dw else groups, **k0), + ConvLayer(nh2, nf, kernel_size, groups=g2, **k1) + ] if expansion == 1 else [ + ConvLayer(ni, nh1, 1, **k0), + ConvLayer(nh1, nh2, kernel_size, stride=stride, groups=nh1 if dw else groups, **k0), + ConvLayer(nh2, nf, 1, groups=g2, **k1)] + self.convs = nn.Sequential(*layers) + convpath = [self.convs] + if reduction: convpath.append(SEModule(nf, reduction=reduction, act_cls=act_cls)) + if sa: convpath.append(SimpleSelfAttention(nf,ks=1,sym=sym)) + self.convpath = nn.Sequential(*convpath) + idpath = [] + if ni!=nf: idpath.append(ConvLayer(ni, nf, 1, act_cls=None, ndim=ndim, **kwargs)) + if stride!=1: idpath.insert((1,0)[pool_first], pool(2, ndim=ndim, ceil_mode=True)) + self.idpath = nn.Sequential(*idpath) + self.act = nn.ReLU(inplace=True) if act_cls is nn.ReLU else act_cls() + + def forward(self, x): return self.act(self.convpath(x) + self.idpath(x)) + + + +# Cell +def init_cnn(m): + if getattr(m, 'bias', None) is not None: nn.init.constant_(m.bias, 0) + if isinstance(m, (nn.Conv1d, nn.Conv2d,nn.Linear)): nn.init.kaiming_normal_(m.weight) + for l in m.children(): init_cnn(l) + +# Cell +class XResNet1d(nn.Sequential): + @delegates(ResBlock) + def __init__(self, block, expansion, layers, p=0.0, input_channels=3, num_classes=1000, stem_szs=(32,32,64),kernel_size=5,kernel_size_stem=5, + widen=1.0, sa=False, act_cls=nn.ReLU, lin_ftrs_head=None, ps_head=0.5, bn_final_head=False, bn_head=True, act_head="relu", concat_pooling=True, **kwargs): + store_attr(self, 'block,expansion,act_cls') + stem_szs = [input_channels, *stem_szs] + stem = [ConvLayer(stem_szs[i], stem_szs[i+1], ks=kernel_size_stem, stride=2 if i==0 else 1, act_cls=act_cls, ndim=1) + for i in range(3)] + + #block_szs = [int(o*widen) for o in [64,128,256,512] +[256]*(len(layers)-4)] + block_szs = [int(o*widen) for o in [64,64,64,64] +[32]*(len(layers)-4)] + block_szs = [64//expansion] + block_szs + blocks = [self._make_layer(ni=block_szs[i], nf=block_szs[i+1], blocks=l, + stride=1 if i==0 else 2, kernel_size=kernel_size, sa=sa and i==len(layers)-4, ndim=1, **kwargs) + for i,l in enumerate(layers)] + + head = create_head1d(block_szs[-1]*expansion, nc=num_classes, lin_ftrs=lin_ftrs_head, ps=ps_head, bn_final=bn_final_head, bn=bn_head, act=act_head, concat_pooling=concat_pooling) + + super().__init__( + *stem, nn.MaxPool1d(kernel_size=3, stride=2, padding=1), + *blocks, + head, + ) + init_cnn(self) + + def _make_layer(self, ni, nf, blocks, stride, kernel_size, sa, **kwargs): + return nn.Sequential( + *[self.block(self.expansion, ni if i==0 else nf, nf, stride=stride if i==0 else 1, + kernel_size=kernel_size, sa=sa and i==(blocks-1), act_cls=self.act_cls, **kwargs) + for i in range(blocks)]) + + def get_layer_groups(self): + return (self[3],self[-1]) + + def get_output_layer(self): + return self[-1][-1] + + def set_output_layer(self,x): + self[-1][-1]=x + +# Cell +def _xresnet1d(expansion, layers, **kwargs): + return XResNet1d(ResBlock, expansion, layers, **kwargs) + +def xresnet1d18 (**kwargs): return _xresnet1d(1, [2, 2, 2, 2], **kwargs) +def xresnet1d34 (**kwargs): return _xresnet1d(1, [3, 4, 6, 3], **kwargs) +def xresnet1d50 (**kwargs): return _xresnet1d(4, [3, 4, 6, 3], **kwargs) +def xresnet1d101(**kwargs): return _xresnet1d(4, [3, 4, 23, 3], **kwargs) +def xresnet1d152(**kwargs): return _xresnet1d(4, [3, 8, 36, 3], **kwargs) +def xresnet1d18_deep (**kwargs): return _xresnet1d(1, [2,2,2,2,1,1], **kwargs) +def xresnet1d34_deep (**kwargs): return _xresnet1d(1, [3,4,6,3,1,1], **kwargs) +def xresnet1d50_deep (**kwargs): return _xresnet1d(4, [3,4,6,3,1,1], **kwargs) +def xresnet1d18_deeper(**kwargs): return _xresnet1d(1, [2,2,1,1,1,1,1,1], **kwargs) +def xresnet1d34_deeper(**kwargs): return _xresnet1d(1, [3,4,6,3,1,1,1,1], **kwargs) +def xresnet1d50_deeper(**kwargs): return _xresnet1d(4, [3,4,6,3,1,1,1,1], **kwargs) \ No newline at end of file