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

Methodforward
(self, x)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:60
Methodforward
(self, x, attn_mask: Optional[torch.Tensor] = None)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:132
Methodforward
(self, x: torch.Tensor)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:202
Methodforward
( self, q_x: torch.Tensor, k_x: Optional[torch.Tensor] = None,
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:254
Methodforward
(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:309
Methodforward
(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:355
Methodforward
(self, x: torch.Tensor, attn_mask: Optional[torch.Tensor] = None)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:418
Methodforward
(self, x: torch.Tensor)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:608
Methodforward
(self, text)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:779
Methodforward
(self, image_embs, text_embs)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:886
Methodforward
( self, image: Optional[torch.Tensor] = None, text: Optional[torch.Tensor]
biomedclip_finetuning/open_clip/src/open_clip/model.py:297
Methodforward
( self, image: Optional[torch.Tensor] = None, text: Optional[torch.Tensor]
biomedclip_finetuning/open_clip/src/open_clip/model.py:375
Methodforward
(self, image, text)
biomedclip_finetuning/open_clip/tests/util_test.py:210
Methodforward
(self, image_features, text_features,batch_size)
loss/hnl.py:21
Methodforward
( ctx: Any, tensor: torch.Tensor, group: Optional["torch.distributed.ProcessGroup"] =
weak_segmentation/nnunetv2/utilities/ddp_allgather.py:28
Methodforward
(self, x, y, loss_mask=None)
weak_segmentation/nnunetv2/training/loss/dice.py:23
Methodforward
(self, x, y, loss_mask=None)
weak_segmentation/nnunetv2/training/loss/dice.py:73
Methodforward
target must be b, c, x, y(, z) with c=1 :param net_output: :param target: :return:
weak_segmentation/nnunetv2/training/loss/compound_losses.py:31
Methodforward
(self, net_output: torch.Tensor, target: torch.Tensor)
weak_segmentation/nnunetv2/training/loss/compound_losses.py:84
Methodforward
target must be b, c, x, y(, z) with c=1 :param net_output: :param target: :return:
weak_segmentation/nnunetv2/training/loss/compound_losses.py:125
Methodforward
(self, *args)
weak_segmentation/nnunetv2/training/loss/deep_supervision.py:17
Methodforward
(self, input: Tensor, target: Tensor)
weak_segmentation/nnunetv2/training/loss/robust_ce_loss.py:12
Functionforward_model
(model, model_name, preprocess_val, image_batch, text_batch)
biomedclip_finetuning/open_clip/tests/util_test.py:37
Methodgenerate
( self, image, text=None, seq_len=30, max_seq_len=77, temperat
biomedclip_finetuning/open_clip/src/open_clip/coca_model.py:202
Methodgenerate_train_batch
(self)
weak_segmentation/nnunetv2/inference/data_iterators.py:145
Methodgenerate_train_batch
(self)
weak_segmentation/nnunetv2/inference/data_iterators.py:191
Methodgenerate_train_batch
(self)
weak_segmentation/nnunetv2/training/dataloading/data_loader_2d.py:7
Methodgenerate_train_batch
(self)
weak_segmentation/nnunetv2/training/dataloading/data_loader_3d.py:7
Functionget_Antropy_all_weights
Retrieves the probability map for a single image from a folder containing multiple checkpoints. Note: this is publication method!! Args:
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:80
Methodget_cast_dtype
(self)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:412
Functionget_csv_dataset
(args, preprocess_fn, is_train, epoch=0, tokenizer=None)
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:446
Methodget_dataloaders
changed order_resampling_data, order_resampling_seg
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDAOrd0.py:10
Methodget_dataloaders
changed order_resampling_data, order_resampling_seg
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDAOrd0.py:59
Methodget_dataloaders
changed order_resampling_data, order_resampling_seg
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDA5.py:309
Methodget_dataloaders
changed order_resampling_data, order_resampling_seg
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerDA5.py:358
Methodget_dataloaders
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/benchmarking/nnUNetTrainerBenchmark_5epochs_noDataLoading.py:24
Functionget_ensemble_name_from_d_tr_c
(dataset, tr1, p1, c1, tr2, p2, c2, folds: Tuple[int, ...])
weak_segmentation/nnunetv2/utilities/file_path_utilities.py:66
Functionget_files_from_folder
Retrieves a list of file paths for files with a '.nii.gz' extension within a folder and its subfolders. Args: folder_path (str): The
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:12
Methodget_image_embedding
Returns the image embeddings for the currently set image, with shape 1xCxHxW, where C is the embedding dimension and (H,W) are
segment-anything/segment_anything/predictor.py:245
Methodget_image_features
r""" Returns: image_features (`torch.FloatTensor` of shape `(batch_size, output_dim`): The image embeddings obtained by
saliency_maps/model/modeling_biomed_clip.py:711
Methodget_image_features
(self, x, output_hidden_states=False, emb_input=False)
saliency_maps/scripts/biomedclip_wrapper.py:216
Methodget_logits
(self, image, text)
biomedclip_finetuning/open_clip/src/open_clip/model.py:288
Methodget_logits
(self, image, text)
biomedclip_finetuning/open_clip/src/open_clip/model.py:366
Functionget_mean_probability_map_for_single_image
Retrieves the mean probability maps for foreground and background for a single image from a folder containing multiple checkpoints. Args:
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:105
Functionget_model_preprocess_cfg
(model)
biomedclip_finetuning/open_clip/src/open_clip/model.py:591
Functionget_model_tokenize_cfg
(model)
biomedclip_finetuning/open_clip/src/open_clip/model.py:615
Methodget_plain_dataloaders
(self, initial_patch_size: Tuple[int, ...], dim: int)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/sampling/nnUNetTrainer_probabilisticOversampling.py:27
Functionget_synthetic_dataset
(args, preprocess_fn, is_train, epoch=0, tokenizer=None)
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:503
Methodget_text_features
r""" Returns: text_features (`torch.FloatTensor` of shape `(batch_size, output_dim`): The text embeddings obtained by
saliency_maps/model/modeling_biomed_clip.py:663
Methodget_text_features
(self, x, output_hidden_states=False, emb_input=False)
saliency_maps/scripts/biomedclip_wrapper.py:219
Methodget_training_transforms
(patch_size: Union[np.ndarray, Tuple[int]], rotation_for_DA: dict,
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoDA.py:11
Methodhas_ignore_label
(self)
weak_segmentation/nnunetv2/utilities/label_handling/label_handling.py:113
Methodhas_regions
(self)
weak_segmentation/nnunetv2/utilities/label_handling/label_handling.py:109
Methodignore_label
(self)
weak_segmentation/nnunetv2/utilities/label_handling/label_handling.py:125
Functionimage_transform
Transformation for CAM (image)
saliency_maps/scripts/utils.py:74
Methodinit_parameters
(self)
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:192
Methodinit_parameters
(self)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:860
Methodinitialize
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/network_architecture/nnUNetTrainerNoDeepSupervision.py:30
Methodinput_size
(self)
biomedclip_finetuning/open_clip/src/open_clip/transform.py:34
Functioninstall_from_zip_entry_point
()
weak_segmentation/nnunetv2/model_sharing/entry_points.py:31
Functioninterpolate_pos_embed
(model, checkpoint_model)
biomedclip_finetuning/open_clip/src/open_clip/pos_embed.py:75
Methodis_complete
(self)
saliency_maps/scripts/iba.py:47
Functionis_pretrained_cfg
(model: str, tag: str)
biomedclip_finetuning/open_clip/src/open_clip/pretrained.py:636
Functionis_using_horovod
()
biomedclip_finetuning/open_clip/src/open_clip_train/distributed.py:54
Functionkeep_running_remote_sync
(sync_every, local_dir, remote_dir, protocol)
biomedclip_finetuning/open_clip/src/open_clip_train/file_utils.py:54
Functionlist_pretrained
returns list of pretrained models Returns a tuple (model_name, pretrain_tag) by default or 'name:tag' if as_str == True
biomedclip_finetuning/open_clip/src/open_clip/pretrained.py:611
Functionload_and_covnert_case
(input_image: str, input_seg: str, output_image: str, output_seg: str, min_component
weak_segmentation/nnunetv2/dataset_conversion/Dataset120_RoadSegmentation.py:14
Functionload_and_covnert_case
(input_image: str, input_seg: str, output_image: str, output_seg: str, min_component
weak_segmentation/nnunetv2/dataset_conversion/our_datasets.py:17
Methodload_checkpoint
(self, filename_or_checkpoint: Union[dict, str])
weak_segmentation/nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py:1089
Functionload_convert_labels_back_to_BraTS
(filename, input_folder, output_folder)
weak_segmentation/nnunetv2/dataset_conversion/Dataset137_BraTS21.py:40
Functionload_niigii_file
(file_path , plot:bool = False)
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:182
Functionload_npz_file
(file_path , plot:bool = False)
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:190
Functionload_openai_model
Load a CLIP model Parameters ---------- name : str A model name listed by `clip.available_models()`, or the path to a model check
biomedclip_finetuning/open_clip/src/open_clip/openai.py:24
Methodload_plans
(self, fname: str)
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py:529
Functionload_postprocess_save
(segmentation_file: str, output_fname: str, image_reader_w
weak_segmentation/nnunetv2/postprocessing/remove_connected_components.py:43
Methodlock
(self, unlocked_groups=0, freeze_bn_stats=False)
biomedclip_finetuning/open_clip/src/open_clip/modified_resnet.py:154
Methodlock
(self, unlocked_layers: int = 0, freeze_layer_norm: bool = True)
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:171
Methodlock
(self, unlocked_groups=0, freeze_bn_stats=False)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:541
Methodlock_image_tower
(self, unlocked_groups=0, freeze_bn_stats=False)
biomedclip_finetuning/open_clip/src/open_clip/model.py:346
Functionlog_and_continue
Call in an exception handler to ignore any exception, issue a warning, and continue.
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:180
Methodmedian_image_size_in_voxels
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:64
Functionmerge
(dict1, dict2)
weak_segmentation/nnunetv2/batch_running/release_trainings/nnunetv2_v1/generate_lsf_commands.py:5
Functionmerge_files
(list_of_files, output_filename_truncated: str, output_file_ending: str,
weak_segmentation/nnunetv2/ensembling/ensemble.py:32
Methodn_conv_per_stage_decoder
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:105
Methodn_conv_per_stage_encoder
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:101
Functionnatural_key
See http://www.codinghorror.com/blog/archives/001018.html
biomedclip_finetuning/open_clip/src/open_clip_train/main.py:49
Methodnext_stage_names
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:168
Methodnormalization_schemes
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:72
Methodnum_channels
(self)
biomedclip_finetuning/open_clip/src/open_clip/transform.py:30
Methodnum_pool_per_axis
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:109
Methodnum_segmentation_heads
(self)
weak_segmentation/nnunetv2/utilities/label_handling/label_handling.py:227
Methodoriginal_median_shape_after_transp
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:243
Methodoriginal_median_spacing_after_transp
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:239
Methodp_zero
(self)
saliency_maps/scripts/iba.py:56
Functionparse
(x)
biomedclip_finetuning/open_clip/src/open_clip/utils.py:50
Methodpatch_size
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:60
Methodperform_actual_validation
(self, save_probabilities: bool = False)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/benchmarking/nnUNetTrainerBenchmark_5epochs.py:18
Functionpermute_then_forward
(self, x)
saliency_maps/scripts/biomedclip_wrapper.py:18
Functionpermute_then_forward
(self, x)
saliency_maps/scripts/clip_wrapper.py:11
Functionplan_experiment_entry
()
weak_segmentation/nnunetv2/experiment_planning/plan_and_preprocess_entrypoints.py:30
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