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

Functioncompute_robust_hausdorff
(surface_distances, percent)
evaluation/SurfaceDice.py:439
Functioncompute_robust_hausdorff
(surface_distances, percent)
weak_segmentation/nnunetv2/evaluation/SurfaceDice.py:439
Functioncompute_surface_overlap_at_tolerance
(surface_distances, tolerance_mm)
evaluation/SurfaceDice.py:460
Functioncompute_surface_overlap_at_tolerance
(surface_distances, tolerance_mm)
weak_segmentation/nnunetv2/evaluation/SurfaceDice.py:460
Methodconfigure_optimizers
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/lr_schedule/nnUNetTrainerCosAnneal.py:8
Methodconfigure_optimizers
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/optimizer/nnUNetTrainerAdan.py:55
Methodconfigure_optimizers
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/optimizer/nnUNetTrainerAdam.py:9
Methodconfigure_optimizers
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/optimizer/nnUNetTrainerAdam.py:21
Methodconfigure_rotation_dummyDA_mirroring_and_inital_patch_size
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoMirroring.py:17
Methodconfigure_rotation_dummyDA_mirroring_and_inital_patch_size
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/data_augmentation/nnUNetTrainerNoDA.py:33
Methodconfigure_rotation_dummyDA_mirroring_and_inital_patch_size
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/training_length/nnUNetTrainer_Xepochs_NoMirroring.py:26
Methodconfigure_rotation_dummyDA_mirroring_and_inital_patch_size
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/training_length/nnUNetTrainer_Xepochs_NoMirroring.py:40
Methodconfigure_rotation_dummyDA_mirroring_and_inital_patch_size
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/variants/training_length/nnUNetTrainer_Xepochs_NoMirroring.py:54
Methodconv_kernel_sizes
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:117
Functionconvert_entry_point
()
weak_segmentation/nnunetv2/dataset_conversion/convert_raw_dataset_from_old_nnunet_format.py:43
Functionconvert_folder_with_preds_back_to_BraTS_labeling_convention
reads all prediction files (nifti) in the input folder, converts the labels back to BraTS convention and saves the
weak_segmentation/nnunetv2/dataset_conversion/Dataset137_BraTS21.py:49
Functionconvert_vision_config
(config: CLIPVisionCfg)
saliency_maps/model/convert.py:65
Functioncount_samples
(dataloader)
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:164
Methoddata_identifier
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:40
Methoddataset_name
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:231
Functiondecode
(output_ids: torch.Tensor)
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:271
Methoddevice
(self)
segment-anything/segment_anything/predictor.py:259
Functiondice_coeff_all_im
Calculate the Dice coefficients for all predicted labels compared to their corresponding true labels. Args: all_predictions_mean (li
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:59
Functiondownload_by_url
()
weak_segmentation/nnunetv2/model_sharing/entry_points.py:18
Methoddraw
(self, renderer, *args, **kwargs)
saliency_maps/scripts/plot.py:13
Methodencode_image
(self, images, normalize: bool = True)
biomedclip_finetuning/open_clip/src/open_clip/coca_model.py:159
Methodencode_text
(self, text, normalize: bool = True)
biomedclip_finetuning/open_clip/src/open_clip/coca_model.py:163
Functionentry_point
()
weak_segmentation/nnunetv2/dataset_conversion/convert_MSD_dataset.py:117
Functionentry_point_apply_postprocessing
()
weak_segmentation/nnunetv2/postprocessing/remove_connected_components.py:318
Functionentry_point_determine_postprocessing_folder
()
weak_segmentation/nnunetv2/postprocessing/remove_connected_components.py:298
Functionentry_point_ensemble_folders
()
weak_segmentation/nnunetv2/ensembling/ensemble.py:114
Functionentry_point_move_plans_between_datasets
()
weak_segmentation/nnunetv2/experiment_planning/plans_for_pretraining/move_plans_between_datasets.py:58
Methodestimate_density
(self, z)
saliency_maps/scripts/iba.py:67
Functionevaluate_folder_entry_point
()
weak_segmentation/nnunetv2/evaluation/evaluate_predictions.py:217
Functionevaluate_simple_entry_point
()
weak_segmentation/nnunetv2/evaluation/evaluate_predictions.py:235
Methodexperiment_planner_class
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:265
Methodexperiment_planner_name
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:273
Functionexport_pretrained_model_entry
()
weak_segmentation/nnunetv2/model_sharing/entry_points.py:41
Functionextract_fingerprint_entry
()
weak_segmentation/nnunetv2/experiment_planning/plan_and_preprocess_entrypoints.py:5
Methodfeed_batch
(self, batch: np.ndarray)
saliency_maps/scripts/iba.py:40
Functionfilter_no_caption_or_no_image
(sample)
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:174
Functionfind_best_configuration_entry_point
()
weak_segmentation/nnunetv2/evaluation/find_best_configuration.py:271
Functionfolds_string_to_tuple
(folds_string: str)
weak_segmentation/nnunetv2/utilities/file_path_utilities.py:85
Methodforeground_intensity_properties_per_channel
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:287
Methodforeground_labels
(self)
weak_segmentation/nnunetv2/utilities/label_handling/label_handling.py:223
Methodforeground_regions
(self)
weak_segmentation/nnunetv2/utilities/label_handling/label_handling.py:219
Methodforward
Predict masks given image and prompt embeddings. Arguments: image_embeddings (torch.Tensor): the embeddings from the i
segment-anything/segment_anything/modeling/mask_decoder.py:71
Methodforward
(self, x)
segment-anything/segment_anything/modeling/mask_decoder.py:171
Methodforward
(self, x: torch.Tensor)
segment-anything/segment_anything/modeling/image_encoder.py:106
Methodforward
(self, x: torch.Tensor)
segment-anything/segment_anything/modeling/image_encoder.py:166
Methodforward
(self, x: torch.Tensor)
segment-anything/segment_anything/modeling/image_encoder.py:224
Methodforward
(self, x: torch.Tensor)
segment-anything/segment_anything/modeling/image_encoder.py:391
Methodforward
(self, x: torch.Tensor)
segment-anything/segment_anything/modeling/common.py:25
Methodforward
(self, x: torch.Tensor)
segment-anything/segment_anything/modeling/common.py:38
Methodforward
Args: image_embedding (torch.Tensor): image to attend to. Should be shape B x embedding_dim x h x w for any h and w.
segment-anything/segment_anything/modeling/transformer.py:62
Methodforward
( self, queries: Tensor, keys: Tensor, query_pe: Tensor, key_pe: Tensor )
segment-anything/segment_anything/modeling/transformer.py:151
Methodforward
(self, q: Tensor, k: Tensor, v: Tensor)
segment-anything/segment_anything/modeling/transformer.py:218
Methodforward
Predicts masks end-to-end from provided images and prompts. If prompts are not known in advance, using SamPredictor is rec
segment-anything/segment_anything/modeling/sam.py:54
Methodforward
Embeds different types of prompts, returning both sparse and dense embeddings. Arguments: points (tuple(torch
segment-anything/segment_anything/modeling/prompt_encoder.py:128
Methodforward
Generate positional encoding for a grid of the specified size.
segment-anything/segment_anything/modeling/prompt_encoder.py:194
Methodforward
( self, image_embeddings: torch.Tensor, point_coords: torch.Tensor, point_
segment-anything/segment_anything/utils/onnx.py:108
Methodforward
( self, input_ids: Optional[torch.LongTensor] = None, token_type_ids: Optional[torch.L
saliency_maps/model/modeling_biomed_clip.py:112
Methodforward
( self, hidden_states: torch.Tensor, attention_mask: Optional[torch.FloatTensor] = Non
saliency_maps/model/modeling_biomed_clip.py:182
Methodforward
(self, hidden_states: torch.Tensor)
saliency_maps/model/modeling_biomed_clip.py:336
Methodforward
( self, hidden_states: torch.Tensor, attention_mask: Optional[torch.FloatTensor] = Non
saliency_maps/model/modeling_biomed_clip.py:358
Methodforward
r""" encoder_hidden_states (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*): Sequence of h
saliency_maps/model/modeling_biomed_clip.py:449
Methodforward
r""" Returns:
saliency_maps/model/modeling_biomed_clip.py:578
Methodforward
r""" Returns: Examples: ```python >>> from PIL import Image >>> import requests >>> from transformer
saliency_maps/model/modeling_biomed_clip.py:759
Methodforward
r""" labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*): Labels for computing the image classification/regression lo
saliency_maps/model/modeling_biomed_clip.py:870
Methodforward
(self, x)
saliency_maps/scripts/biomedclip_wrapper.py:125
Methodforward
(self, x, output_hidden_states=False, emb_input=False)
saliency_maps/scripts/biomedclip_wrapper.py:150
Methodforward
(self, text)
saliency_maps/scripts/biomedclip_wrapper.py:171
Methodforward
(self, x, output_hidden_states=False, emb_input=False)
saliency_maps/scripts/biomedclip_wrapper.py:192
Methodforward
(self, *input, **kwargs)
saliency_maps/scripts/utils.py:16
Methodforward
(self, x)
saliency_maps/scripts/clip_wrapper.py:26
Methodforward
(self, x, output_hidden_states=False, emb_input = False)
saliency_maps/scripts/clip_wrapper.py:46
Methodforward
(self, text)
saliency_maps/scripts/clip_wrapper.py:72
Methodforward
(self, x, output_hidden_states=False, emb_input=False)
saliency_maps/scripts/clip_wrapper.py:90
Methodforward
(self, x, **kwargs)
saliency_maps/scripts/iba.py:120
Methodforward
(self, image_features, text_features, logit_scale, output_dict=False)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:150
Methodforward
(self, image_features, text_features, logits, labels, logit_scale, output_dict=False)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:211
Methodforward
( self, image_features, text_features, logit_scale,
biomedclip_finetuning/open_clip/src/open_clip/loss.py:236
Methodforward
(ctx, from_rank, to_rank, group, tensor)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:325
Methodforward
(ctx, left_rank, right_rank, group, tensor_to_left, tensor_to_right)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:342
Methodforward
(self, image_features, text_features, logit_scale, logit_bias, output_dict=False)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:411
Methodforward
( self, image, text: Optional[torch.Tensor] = None, image_late
biomedclip_finetuning/open_clip/src/open_clip/coca_model.py:167
Methodforward
(self, x: torch.Tensor)
biomedclip_finetuning/open_clip/src/open_clip/modified_resnet.py:42
Methodforward
(self, x)
biomedclip_finetuning/open_clip/src/open_clip/modified_resnet.py:68
Methodforward
(self, x)
biomedclip_finetuning/open_clip/src/open_clip/modified_resnet.py:173
Methodforward
Args: img (PIL Image or Tensor): Image to be cropped. Returns: PIL Image or Tensor: Cropped image.
biomedclip_finetuning/open_clip/src/open_clip/transform.py:224
Methodforward
(self, x)
biomedclip_finetuning/open_clip/src/open_clip/timm_model.py:150
Methodforward
(self, x: BaseModelOutput, attention_mask: TensorType)
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:49
Methodforward
(self, x: BaseModelOutput, attention_mask: TensorType)
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:58
Methodforward
(self, x: BaseModelOutput, attention_mask: TensorType)
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:72
Methodforward
(self, x: BaseModelOutput, attention_mask: TensorType)
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:92
Methodforward
(self, x: TensorType)
biomedclip_finetuning/open_clip/src/open_clip/hf_model.py:154
Methodforward
(self, x: torch.Tensor)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:18
Methodforward
(self, x: torch.Tensor)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:27
Methodforward
(self, x: torch.Tensor)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:35
Methodforward
(self, x)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:45
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