SYMBOL INDEX (230 symbols across 13 files) FILE: data_preprocess.py function ResampleXYZAxis (line 7) | def ResampleXYZAxis(imImage, space=(1., 1., 1.), interp=sitk.sitkLinear): function ResampleFullImageToRef (line 23) | def ResampleFullImageToRef(imImage, imRef, interp=sitk.sitkNearestNeighb... function ResampleCMRImage (line 37) | def ResampleCMRImage(imImage, imLabel, save_path, patient_name, name, ta... FILE: dataset_domain.py class CMRDataset (line 13) | class CMRDataset(Dataset): method __init__ (line 14) | def __init__(self, dataset_dir, mode='train', domain='A', crop_size=25... method __len__ (line 103) | def __len__(self): method preprocess (line 106) | def preprocess(self, itk_img, itk_lab): method __getitem__ (line 131) | def __getitem__(self, idx): method randcrop (line 162) | def randcrop(self, img, label): method center_crop (line 177) | def center_crop(self, img, label): method random_zoom_rotate (line 191) | def random_zoom_rotate(self, img, label): FILE: losses.py class DiceLoss (line 8) | class DiceLoss(nn.Module): method __init__ (line 10) | def __init__(self, alpha=0.5, beta=0.5, size_average=True, reduce=True): method forward (line 18) | def forward(self, preds, targets): class FocalLoss (line 60) | class FocalLoss(nn.Module): method __init__ (line 61) | def __init__(self, class_num, alpha=None, gamma=2, size_average=True): method forward (line 72) | def forward(self, preds, targets): FILE: model/conv_trans_utils.py function conv3x3 (line 9) | def conv3x3(in_planes, out_planes, stride=1): function conv1x1 (line 11) | def conv1x1(in_planes, out_planes, stride=1): class depthwise_separable_conv (line 14) | class depthwise_separable_conv(nn.Module): method __init__ (line 15) | def __init__(self, in_ch, out_ch, stride=1, kernel_size=3, padding=1, ... method forward (line 20) | def forward(self, x): class Mlp (line 26) | class Mlp(nn.Module): method __init__ (line 27) | def __init__(self, in_ch, hid_ch=None, out_ch=None, act_layer=nn.GELU,... method forward (line 37) | def forward(self, x): class BasicBlock (line 46) | class BasicBlock(nn.Module): method __init__ (line 48) | def __init__(self, inplanes, planes, stride=1): method forward (line 65) | def forward(self, x): class BasicTransBlock (line 80) | class BasicTransBlock(nn.Module): method __init__ (line 82) | def __init__(self, in_ch, heads, dim_head, attn_drop=0., proj_drop=0.,... method forward (line 93) | def forward(self, x): class BasicTransDecoderBlock (line 109) | class BasicTransDecoderBlock(nn.Module): method __init__ (line 111) | def __init__(self, in_ch, out_ch, heads, dim_head, attn_drop=0., proj_... method forward (line 124) | def forward(self, x1, x2): class LinearAttention (line 150) | class LinearAttention(nn.Module): method __init__ (line 152) | def __init__(self, dim, heads=4, dim_head=64, attn_drop=0., proj_drop=... method forward (line 180) | def forward(self, x): class LinearAttentionDecoder (line 217) | class LinearAttentionDecoder(nn.Module): method __init__ (line 219) | def __init__(self, in_dim, out_dim, heads=4, dim_head=64, attn_drop=0.... method forward (line 247) | def forward(self, q, x): class RelativePositionEmbedding (line 284) | class RelativePositionEmbedding(nn.Module): method __init__ (line 286) | def __init__(self, dim, shape): method forward (line 303) | def forward(self, q, Nh, H, W, dim_head): method relative_logits_1d (line 316) | def relative_logits_1d(self, q, rel_k, case): class RelativePositionBias (line 344) | class RelativePositionBias(nn.Module): method __init__ (line 348) | def __init__(self, num_heads, h, w): method forward (line 371) | def forward(self, H, W): class down_block_trans (line 385) | class down_block_trans(nn.Module): method __init__ (line 386) | def __init__(self, in_ch, out_ch, num_block, bottleneck=False, maxpool... method forward (line 411) | def forward(self, x): class up_block_trans (line 418) | class up_block_trans(nn.Module): method __init__ (line 419) | def __init__(self, in_ch, out_ch, num_block, bottleneck=False, heads=4... method forward (line 439) | def forward(self, x1, x2): class block_trans (line 447) | class block_trans(nn.Module): method __init__ (line 448) | def __init__(self, in_ch, num_block, heads=4, dim_head=64, attn_drop=0... method forward (line 462) | def forward(self, x): FILE: model/resnet_utnet.py class ResNet_UTNet (line 13) | class ResNet_UTNet(nn.Module): method __init__ (line 14) | def __init__(self, in_ch, num_class, reduce_size=8, block_list='234', ... method forward (line 51) | def forward(self, x): FILE: model/swin_unet.py class Mlp (line 48) | class Mlp(nn.Module): method __init__ (line 50) | def __init__(self, in_features, hidden_features=None, out_features=Non... method forward (line 68) | def forward(self, x): function window_partition (line 86) | def window_partition(x, window_size): function window_reverse (line 116) | def window_reverse(windows, window_size, H, W): class WindowAttention (line 150) | class WindowAttention(nn.Module): method __init__ (line 178) | def __init__(self, dim, window_size, num_heads, qkv_bias=True, qk_scal... method forward (line 246) | def forward(self, x, mask=None): method extra_repr (line 312) | def extra_repr(self) -> str: method flops (line 318) | def flops(self, N): class SwinTransformerBlock (line 346) | class SwinTransformerBlock(nn.Module): method __init__ (line 384) | def __init__(self, dim, input_resolution, num_heads, window_size=7, sh... method forward (line 486) | def forward(self, x): method extra_repr (line 564) | def extra_repr(self) -> str: method flops (line 571) | def flops(self): class PatchMerging (line 601) | class PatchMerging(nn.Module): method __init__ (line 619) | def __init__(self, input_resolution, dim, norm_layer=nn.LayerNorm): method forward (line 633) | def forward(self, x): method extra_repr (line 679) | def extra_repr(self) -> str: method flops (line 685) | def flops(self): class PatchExpand (line 697) | class PatchExpand(nn.Module): method __init__ (line 699) | def __init__(self, input_resolution, dim, dim_scale=2, norm_layer=nn.L... method forward (line 713) | def forward(self, x): class FinalPatchExpand_X4 (line 745) | class FinalPatchExpand_X4(nn.Module): method __init__ (line 747) | def __init__(self, input_resolution, dim, dim_scale=4, norm_layer=nn.L... method forward (line 765) | def forward(self, x): class BasicLayer (line 797) | class BasicLayer(nn.Module): method __init__ (line 837) | def __init__(self, dim, input_resolution, depth, num_heads, window_size, method forward (line 893) | def forward(self, x): method extra_repr (line 913) | def extra_repr(self) -> str: method flops (line 919) | def flops(self): class BasicLayer_up (line 935) | class BasicLayer_up(nn.Module): method __init__ (line 975) | def __init__(self, dim, input_resolution, depth, num_heads, window_size, method forward (line 1031) | def forward(self, x): class PatchEmbed (line 1051) | class PatchEmbed(nn.Module): method __init__ (line 1073) | def __init__(self, img_size=224, patch_size=4, in_chans=3, embed_dim=9... method forward (line 1111) | def forward(self, x): method flops (line 1130) | def flops(self): class SwinTransformerSys (line 1146) | class SwinTransformerSys(nn.Module): method __init__ (line 1198) | def __init__(self, img_size=224, patch_size=4, in_chans=3, num_classes... method _init_weights (line 1384) | def _init_weights(self, m): method no_weight_decay (line 1404) | def no_weight_decay(self): method no_weight_decay_keywords (line 1412) | def no_weight_decay_keywords(self): method forward_features (line 1420) | def forward_features(self, x): method forward_up_features (line 1452) | def forward_up_features(self, x, x_downsample): method up_x4 (line 1478) | def up_x4(self, x): method forward (line 1504) | def forward(self, x): method flops (line 1518) | def flops(self): class SwinUnet_config (line 1541) | class SwinUnet_config(): method __init__ (line 1542) | def __init__(self): class SwinUnet (line 1559) | class SwinUnet(nn.Module): method __init__ (line 1561) | def __init__(self, config, img_size=224, num_classes=21843, zero_head=... method forward (line 1607) | def forward(self, x): method load_from (line 1619) | def load_from(self, pretrained_path): FILE: model/transunet.py function np2th (line 72) | def np2th(weights, conv=False): function swish (line 86) | def swish(x): class Attention (line 100) | class Attention(nn.Module): method __init__ (line 102) | def __init__(self, config, vis): method transpose_for_scores (line 136) | def transpose_for_scores(self, x): method forward (line 146) | def forward(self, hidden_states): class Mlp (line 194) | class Mlp(nn.Module): method __init__ (line 196) | def __init__(self, config): method _init_weights (line 214) | def _init_weights(self): method forward (line 226) | def forward(self, x): class Embeddings (line 244) | class Embeddings(nn.Module): method __init__ (line 250) | def __init__(self, config, img_size, in_channels=3): method forward (line 308) | def forward(self, x): class Block (line 336) | class Block(nn.Module): method __init__ (line 338) | def __init__(self, config, vis): method forward (line 354) | def forward(self, x): method load_from (line 378) | def load_from(self, weights, n_block): class Encoder (line 454) | class Encoder(nn.Module): method __init__ (line 456) | def __init__(self, config, vis): method forward (line 474) | def forward(self, hidden_states): class Transformer (line 494) | class Transformer(nn.Module): method __init__ (line 496) | def __init__(self, config, img_size, vis): method forward (line 506) | def forward(self, input_ids): class Conv2dReLU (line 518) | class Conv2dReLU(nn.Sequential): method __init__ (line 520) | def __init__( class DecoderBlock (line 568) | class DecoderBlock(nn.Module): method __init__ (line 570) | def __init__( method forward (line 618) | def forward(self, x, skip=None): class SegmentationHead (line 636) | class SegmentationHead(nn.Sequential): method __init__ (line 640) | def __init__(self, in_channels, out_channels, kernel_size=3, upsamplin... class DecoderCup (line 652) | class DecoderCup(nn.Module): method __init__ (line 654) | def __init__(self, config): method forward (line 710) | def forward(self, hidden_states, features=None): class VisionTransformer (line 740) | class VisionTransformer(nn.Module): method __init__ (line 742) | def __init__(self, config, img_size=224, num_classes=21843, zero_head=... method forward (line 770) | def forward(self, x): method load_from (line 786) | def load_from(self, weights): function get_b16_config (line 885) | def get_b16_config(): function get_testing (line 934) | def get_testing(): function get_r50_b16_config (line 964) | def get_r50_b16_config(): function get_b32_config (line 1002) | def get_b32_config(): function get_l16_config (line 1018) | def get_l16_config(): function get_r50_l16_config (line 1064) | def get_r50_l16_config(): function get_l32_config (line 1098) | def get_l32_config(): function get_h14_config (line 1112) | def get_h14_config(): function np2th (line 1176) | def np2th(weights, conv=False): class StdConv2d (line 1190) | class StdConv2d(nn.Conv2d): method forward (line 1194) | def forward(self, x): function conv3x3 (line 1210) | def conv3x3(cin, cout, stride=1, groups=1, bias=False): function conv1x1 (line 1220) | def conv1x1(cin, cout, stride=1, bias=False): class PreActBottleneck (line 1230) | class PreActBottleneck(nn.Module): method __init__ (line 1238) | def __init__(self, cin, cout=None, cmid=None, stride=1): method forward (line 1274) | def forward(self, x): method load_from (line 1306) | def load_from(self, weights, n_block, n_unit): class ResNetV2 (line 1378) | class ResNetV2(nn.Module): method __init__ (line 1384) | def __init__(self, block_units, width_factor): method forward (line 1438) | def forward(self, x): FILE: model/unet_utils.py class DoubleConv (line 6) | class DoubleConv(nn.Module): method __init__ (line 12) | def __init__(self, in_channels, out_channels, mid_channels=None): method forward (line 38) | def forward(self, x): class Down (line 46) | class Down(nn.Module): method __init__ (line 52) | def __init__(self, in_channels, out_channels): method forward (line 66) | def forward(self, x): class Up (line 74) | class Up(nn.Module): method __init__ (line 80) | def __init__(self, in_channels, out_channels, bilinear=True): method forward (line 104) | def forward(self, x1, x2): class OutConv (line 134) | class OutConv(nn.Module): method __init__ (line 136) | def __init__(self, in_channels, out_channels): method forward (line 144) | def forward(self, x): function conv3x3 (line 149) | def conv3x3(in_planes, out_planes, stride=1): function conv1x1 (line 151) | def conv1x1(in_planes, out_planes, stride=1): class BasicBlock (line 156) | class BasicBlock(nn.Module): method __init__ (line 158) | def __init__(self, inplanes, planes, stride=1): method forward (line 175) | def forward(self, x): class BottleneckBlock (line 190) | class BottleneckBlock(nn.Module): method __init__ (line 192) | def __init__(self, inplanes, planes, stride=1): method forward (line 212) | def forward(self, x): class inconv (line 233) | class inconv(nn.Module): method __init__ (line 234) | def __init__(self, in_ch, out_ch, bottleneck=False): method forward (line 244) | def forward(self, x): class down_block (line 251) | class down_block(nn.Module): method __init__ (line 252) | def __init__(self, in_ch, out_ch, scale, num_block, bottleneck=False, ... method forward (line 274) | def forward(self, x): class up_block (line 280) | class up_block(nn.Module): method __init__ (line 281) | def __init__(self, in_ch, out_ch, num_block, scale=(2,2),bottleneck=Fa... method forward (line 301) | def forward(self, x1, x2): FILE: model/utnet.py class UTNet (line 11) | class UTNet(nn.Module): method __init__ (line 13) | def __init__(self, in_chan, base_chan, num_classes=1, reduce_size=8, b... method forward (line 66) | def forward(self, x): class UTNet_Encoderonly (line 105) | class UTNet_Encoderonly(nn.Module): method __init__ (line 107) | def __init__(self, in_chan, base_chan, num_classes=1, reduce_size=8, b... method forward (line 158) | def forward(self, x): FILE: train_deep.py function train_net (line 28) | def train_net(net, options): function validation (line 141) | def validation(net, test_loader, options): function cal_distance (line 187) | def cal_distance(label_pred, label_true, spacing): function get_comma_separated_int_args (line 210) | def get_comma_separated_int_args(option, opt, value, parser): FILE: utils/lookup_tables.py function create_table_neighbour_code_to_surface_area (line 591) | def create_table_neighbour_code_to_surface_area(spacing_mm): function create_table_neighbour_code_to_contour_length (line 655) | def create_table_neighbour_code_to_contour_length(spacing_mm): FILE: utils/metrics.py function _assert_is_numpy_array (line 49) | def _assert_is_numpy_array(name, array): function _check_nd_numpy_array (line 63) | def _check_nd_numpy_array(name, array, num_dims): function _check_2d_numpy_array (line 77) | def _check_2d_numpy_array(name, array): function _check_3d_numpy_array (line 85) | def _check_3d_numpy_array(name, array): function _assert_is_bool_numpy_array (line 93) | def _assert_is_bool_numpy_array(name, array): function _compute_bounding_box (line 107) | def _compute_bounding_box(mask): function _crop_to_bounding_box (line 187) | def _crop_to_bounding_box(mask, bbox_min, bbox_max): function _sort_distances_surfels (line 237) | def _sort_distances_surfels(distances, surfel_areas): function compute_surface_distances (line 265) | def compute_surface_distances(mask_gt, function compute_average_surface_distance (line 579) | def compute_average_surface_distance(surface_distances): function compute_robust_hausdorff (line 641) | def compute_robust_hausdorff(surface_distances, percent): function compute_surface_overlap_at_tolerance (line 723) | def compute_surface_overlap_at_tolerance(surface_distances, tolerance_mm): function compute_surface_dice_at_tolerance (line 785) | def compute_surface_dice_at_tolerance(surface_distances, tolerance_mm): function compute_dice_coefficient (line 845) | def compute_dice_coefficient(mask_gt, mask_pred): FILE: utils/utils.py function log_evaluation_result (line 9) | def log_evaluation_result(writer, dice_list, ASD_list, HD_list, name, ep... function multistep_lr_scheduler_with_warmup (line 22) | def multistep_lr_scheduler_with_warmup(optimizer, init_lr, epoch, warmup... function exp_lr_scheduler_with_warmup (line 49) | def exp_lr_scheduler_with_warmup(optimizer, init_lr, epoch, warmup_epoch... function cal_dice (line 69) | def cal_dice(pred, target, C): function cal_asd (line 91) | def cal_asd(itkPred, itkGT):