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Functions1,090 in github.com/HealthX-Lab/MedCLIP-SAMv2

Method__call__
(self, x)
saliency_maps/scripts/utils.py:62
Method__call__
(self, x)
saliency_maps/scripts/utils.py:71
Method__call__
Returns the tokenized representation of given input string(s) Parameters ---------- texts : Union[str, List[str]]
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:226
Method__call__
(self, texts: Union[str, List[str]], context_length: Optional[int] = None)
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:430
Method__call__
(self, texts: Union[str, List[str]], context_length: Optional[int] = None)
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:504
Method__call__
Args: img (PIL Image): Image to be cropped and resized. Returns: PIL Image: Resized, padded to at least targ
biomedclip_finetuning/open_clip/src/open_clip/transform.py:144
Method__call__
(self, img)
biomedclip_finetuning/open_clip/src/open_clip/transform.py:251
Method__call__
(self, img)
biomedclip_finetuning/open_clip/src/open_clip/transform.py:267
Method__call__
(self, parser, namespace, values, option_string=None)
biomedclip_finetuning/open_clip/src/open_clip_train/params.py:15
Method__call__
(self, module)
weak_segmentation/nnunetv2/utilities/network_initialization.py:8
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/masking.py:18
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/transforms_for_dummy_2d.py:13
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/transforms_for_dummy_2d.py:33
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/deep_supervision_donwsampling.py:27
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/manipulating_data_dict.py:8
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/cascade_transforms.py:23
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/cascade_transforms.py:58
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/cascade_transforms.py:111
Method__call__
(self, **data_dict)
weak_segmentation/nnunetv2/training/data_augmentation/custom_transforms/region_based_training.py:23
Method__delitem__
(self, key: str)
segment-anything/segment_anything/utils/amg.py:35
Method__enter__
(self)
weak_segmentation/nnunetv2/utilities/helpers.py:24
Method__exit__
(self, exc_type, exc_val, exc_tb)
weak_segmentation/nnunetv2/utilities/helpers.py:27
Method__getitem__
(self, key: str)
segment-anything/segment_anything/utils/amg.py:38
Method__getitem__
(self, idx)
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:44
Method__getitem__
(self, idx)
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:497
Method__getitem__
(self, key)
weak_segmentation/nnunetv2/training/dataloading/nnunet_dataset.py:59
Method__init__
Uses SAM to calculate the image embedding for an image, and then allow repeated, efficient mask prediction given prompts.
segment-anything/segment_anything/predictor.py:18
Method__init__
Using a SAM model, generates masks for the entire image. Generates a grid of point prompts over the image, then filters lo
segment-anything/segment_anything/automatic_mask_generator.py:36
Method__init__
Predicts masks given an image and prompt embeddings, using a transformer architecture. Arguments: transformer
segment-anything/segment_anything/modeling/mask_decoder.py:17
Method__init__
Args: img_size (int): Input image size. patch_size (int): Patch size. in_chans (int): Number of input
segment-anything/segment_anything/modeling/image_encoder.py:18
Method__init__
Args: dim (int): Number of input channels. num_heads (int): Number of attention heads. qkv_bias (bool
segment-anything/segment_anything/modeling/image_encoder.py:188
Method__init__
Args: kernel_size (Tuple): kernel size of the projection layer. stride (Tuple): stride of the projection layer.
segment-anything/segment_anything/modeling/image_encoder.py:369
Method__init__
(self, num_channels: int, eps: float = 1e-6)
segment-anything/segment_anything/modeling/common.py:32
Method__init__
A transformer decoder that attends to an input image using queries whose positional embedding is supplied. Args:
segment-anything/segment_anything/modeling/transformer.py:17
Method__init__
A transformer block with four layers: (1) self-attention of sparse inputs, (2) cross attention of sparse inputs to dense inputs, (3
segment-anything/segment_anything/modeling/transformer.py:110
Method__init__
SAM predicts object masks from an image and input prompts. Arguments: image_encoder (ImageEncoderViT): The backbone us
segment-anything/segment_anything/modeling/sam.py:22
Method__init__
(self, num_pos_feats: int = 64, scale: Optional[float] = None)
segment-anything/segment_anything/modeling/prompt_encoder.py:176
Method__init__
(self, target_length: int)
segment-anything/segment_anything/utils/transforms.py:23
Method__init__
( self, model: Sam, return_single_mask: bool, use_stability_score: bool =
segment-anything/segment_anything/utils/onnx.py:25
Method__init__
(self, **kwargs)
segment-anything/segment_anything/utils/amg.py:22
Method__init__
(self, config: CLIPVisionConfig)
saliency_maps/model/modeling_biomed_clip.py:77
Method__init__
(self, config: CLIPTextConfig)
saliency_maps/model/modeling_biomed_clip.py:91
Method__init__
(self, config, position_embedding_type=None)
saliency_maps/model/modeling_biomed_clip.py:157
Method__init__
(self, config: BiomedCLIPConfig, norm='pre')
saliency_maps/model/modeling_biomed_clip.py:235
Method__init__
(self, config)
saliency_maps/model/modeling_biomed_clip.py:329
Method__init__
(self, config, norm='pre')
saliency_maps/model/modeling_biomed_clip.py:351
Method__init__
(self, config: CLIPTextConfig)
saliency_maps/model/modeling_biomed_clip.py:438
Method__init__
(self, config: CLIPVisionConfig)
saliency_maps/model/modeling_biomed_clip.py:567
Method__init__
(self, config: BiomedCLIPConfig)
saliency_maps/model/modeling_biomed_clip.py:856
Method__init__
( self, hidden_size=768, intermediate_size=640, projection_dim=512, nu
saliency_maps/model/configuration_biomed_clip.py:7
Method__init__
(self, cls_token, patch_embed, pos_embed, dtype)
saliency_maps/scripts/biomedclip_wrapper.py:118
Method__init__
(self, model, dtype)
saliency_maps/scripts/biomedclip_wrapper.py:135
Method__init__
(self, token_embedding, positional_embedding, dtype)
saliency_maps/scripts/biomedclip_wrapper.py:165
Method__init__
(self, model)
saliency_maps/scripts/biomedclip_wrapper.py:177
Method__init__
(self, model)
saliency_maps/scripts/utils.py:58
Method__init__
(self, model)
saliency_maps/scripts/utils.py:67
Method__init__
(self, class_embedding, patch_embedding, positional_embedding, dtype)
saliency_maps/scripts/clip_wrapper.py:19
Method__init__
(self, model, dtype)
saliency_maps/scripts/clip_wrapper.py:35
Method__init__
(self, token_embedding, positional_embedding, dtype)
saliency_maps/scripts/clip_wrapper.py:66
Method__init__
(self, model)
saliency_maps/scripts/clip_wrapper.py:78
Method__init__
(self, mean: np.ndarray, std: np.ndarray, device=None)
saliency_maps/scripts/iba.py:90
Method__init__
(self, model, estim: Estimator, beta, steps=10, lr=1, batch_size=10, ensemble=False, progbar=False)
saliency_maps/scripts/iba.py:131
Method__init__
(self, x, y, text, bgcolor, *args, **kwargs)
saliency_maps/scripts/plot.py:9
Method__init__
(self, temperature=1.0,beta1=1.0, beta2 = 1.0, alpha=0.0, batch_size=1)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:142
Method__init__
( self, caption_loss_weight, clip_loss_weight, pad_id=0, # pa
biomedclip_finetuning/open_clip/src/open_clip/loss.py:186
Method__init__
( self, cache_labels=False, rank=0, world_size=1,
biomedclip_finetuning/open_clip/src/open_clip/loss.py:368
Method__init__
( self, embed_dim, multimodal_cfg: MultimodalCfg, text_cfg: CL
biomedclip_finetuning/open_clip/src/open_clip/coca_model.py:90
Method__init__
(self, spacial_dim: int, embed_dim: int, num_heads: int, output_dim: int = None)
biomedclip_finetuning/open_clip/src/open_clip/modified_resnet.py:59
Method__init__
(self, layers, output_dim, heads, image_size=224, width=64)
biomedclip_finetuning/open_clip/src/open_clip/modified_resnet.py:103
Method__init__
( self, bpe_path: str = default_bpe(), additional_special_tokens: Optional
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:134
Method__init__
( self, tokenizer_name: str, context_length: Optional[int] = DEFAULT_CONTE
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:406
Method__init__
( self, tokenizer_name: str, context_length: Optional[int] = 64, )
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:477
Method__init__
( self, size, longest=0., interpolation=InterpolationMode.BICU
biomedclip_finetuning/open_clip/src/open_clip/transform.py:94
Method__init__
(self, size, fill=0)
biomedclip_finetuning/open_clip/src/open_clip/transform.py:219
Method__init__
(self, brightness=0., contrast=0., saturation=0., hue=0., p=0.8)
biomedclip_finetuning/open_clip/src/open_clip/transform.py:246
Method__init__
( self, model_name, embed_dim, image_size=224, poo
biomedclip_finetuning/open_clip/src/open_clip/timm_model.py:33
Method__init__
(self)
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:88
Method__init__
( self, model_name_or_path: str, output_dim: int, config: Pret
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:100
Method__init__
(self, dim, init_values=1e-5, inplace=False)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:40
Method__init__
(self, prob, exclude_first_token=True)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:54
Method__init__
( self, d_model: int, context_dim: int, n_head: int = 8,
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:188
Method__init__
( self, d_model: int, n_head: int, mlp_ratio: float = 4.0,
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:211
Method__init__
( self, d_model: int, n_head: int, mlp_ratio: float = 4.0,
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:269
Method__init__
( self, width: int, layers: int, heads: int, mlp_r
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:320
Method__init__
( self, width: int, layers: int, heads: int, mlp_r
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:371
Method__init__
( self, image_size: int, patch_size: int, width: int,
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:437
Method__init__
( self, context_length: int = 77, vocab_size: int = 49408, wid
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:671
Method__init__
( self, width: int, layers: int, heads: int, conte
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:817
Method__init__
( self, embed_dim: int, vision_cfg: CLIPVisionCfg, text_cfg: C
biomedclip_finetuning/open_clip/src/open_clip/model.py:323
Method__init__
(self)
biomedclip_finetuning/open_clip/src/open_clip_train/train.py:26
Method__init__
(self, epoch: int = 0)
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:51
Method__init__
( self, bufsize=1000, initial=100, seed=0, epoch=-
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:243
Method__init__
Sample shards from the shard list with replacement. :param urls: a list of URLs as a Python list or brace notation string
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:277
Method__init__
( self, transform=None, image_size=(224, 224), caption="Dummy
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:478
Method__init__
(self, model, model_name, output_dict=True)
biomedclip_finetuning/open_clip/tests/util_test.py:201
Method__init__
(self, temperature=1.0,beta1=1.0, beta2 = 1.0, alpha=0)
loss/hnl.py:14
Method__init__
extracts the dataset fingerprint used for experiment planning. The dataset fingerprint will be saved as a json file in the input_fold
weak_segmentation/nnunetv2/experiment_planning/dataset_fingerprint/fingerprint_extractor.py:20
Method__init__
overwrite_target_spacing only affects 3d_fullres! (but by extension 3d_lowres which starts with fullres may also be affected
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py:23
Method__init__
(self, dataset_name_or_id: Union[str, int], gpu_memory_target_in_gb: float = 8,
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/resencUNet_planner.py:10
Method__init__
(self, verbose: bool = True)
weak_segmentation/nnunetv2/preprocessing/preprocessors/default_preprocessor.py:34
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