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

↓ 1 callersFunctiondefault_bpe
()
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:27
↓ 1 callersMethoddetermine_normalization_scheme_and_whether_mask_is_used_for_norm
(self)
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py:199
↓ 1 callersMethoddetermine_reader_writer
(self)
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py:79
↓ 1 callersMethoddetermine_resampling
returns what functions to use for resampling data and seg, respectively. Also returns kwargs resampling function must be callable(dat
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py:114
↓ 1 callersMethoddetermine_segmentation_softmax_export_fn
function must be callable(data, new_shape, current_spacing, new_spacing, **kwargs). The new_shape should be used as target. current_s
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py:138
↓ 1 callersMethoddetermine_shapes
(self)
weak_segmentation/nnunetv2/training/dataloading/base_data_loader.py:55
↓ 1 callersMethoddetermine_transpose
(self)
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/default_experiment_planner.py:216
↓ 1 callersFunctiondice
(pred_array, label_array)
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:199
↓ 1 callersFunctiondice_coefficient
Calculates the Dice coefficient, a measure of similarity, between two binary label volumes. Note: the dice output is per image and per checkp
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:36
↓ 1 callersFunctiondownload_and_install_from_url
(url)
weak_segmentation/nnunetv2/model_sharing/model_download.py:11
↓ 1 callersFunctiondownload_file
(url: str, local_filename: str, chunk_size: Optional[int] = 8192 * 16)
weak_segmentation/nnunetv2/model_sharing/model_download.py:37
↓ 1 callersFunctiondownload_pretrained
( cfg: Dict, prefer_hf_hub: bool = True, cache_dir: Optional[str] = None, )
biomedclip_finetuning/open_clip/src/open_clip/pretrained.py:758
↓ 1 callersFunctionensemble_crossvalidations
Feature: different configurations can now have different splits
weak_segmentation/nnunetv2/ensembling/ensemble.py:128
↓ 1 callersFunctionentropy_map_fun
(fg_map, bg_map)
weak_segmentation/nnunetv2/nnunet/uncertainty_utils.py:134
↓ 1 callersFunctionentry_point_generate_overlay
()
weak_segmentation/nnunetv2/utilities/overlay_plots.py:242
↓ 1 callersFunctionevaluate_on_sample
(model, processor, tokenizer, text, image_paths, args)
saliency_maps/generate_saliency_maps.py:35
↓ 1 callersFunctionexample_test_case_preprocessing
()
weak_segmentation/nnunetv2/preprocessing/preprocessors/default_preprocessor.py:271
↓ 1 callersFunctionexport_prediction_from_logits
(predicted_array_or_file: Union[np.ndarray, torch.Tensor], properties_dict: dict,
weak_segmentation/nnunetv2/inference/export_prediction.py:71
↓ 1 callersFunctionextract_feature_map
(model, layer_idx, x)
saliency_maps/scripts/methods.py:13
↓ 1 callersFunctionextract_fingerprint_dataset
Returns the fingerprint as a dictionary (additionally to saving it)
weak_segmentation/nnunetv2/experiment_planning/plan_and_preprocess_api.py:17
↓ 1 callersFunctionextract_text_feature_map
(model, layer_idx, x)
saliency_maps/scripts/methods.py:19
↓ 1 callersMethodfeed
(self, z: np.ndarray)
saliency_maps/scripts/iba.py:25
↓ 1 callersFunctionfilter_available_models
(model_dict: Union[List[dict], Tuple[dict, ...]], dataset_name_or_id: Union[str, int])
weak_segmentation/nnunetv2/evaluation/find_best_configuration.py:26
↓ 1 callersFunctionfind_free_network_port
Finds a free port on localhost. It is useful in single-node training when we don't want to connect to a real main node but have to set the `M
weak_segmentation/nnunetv2/run/run_training.py:18
↓ 1 callersMethodforward
(self, image_features, text_features, logit_scale, output_dict=False)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:120
↓ 1 callersMethodforward
(self, inp, target)
weak_segmentation/nnunetv2/training/loss/robust_ce_loss.py:27
↓ 1 callersFunctiongather_features
( image_features, text_features, local_loss=False, gather_with_grad=False,
biomedclip_finetuning/open_clip/src/open_clip/loss.py:19
↓ 1 callersMethodgenerate
Generates masks for the given image. Arguments: image (np.ndarray): The image to generate masks for, in HWC uint8 form
segment-anything/segment_anything/automatic_mask_generator.py:137
↓ 1 callersFunctiongenerate_crop_boxes
Generates a list of crop boxes of different sizes. Each layer has (2**i)**2 boxes for the ith layer.
segment-anything/segment_anything/utils/amg.py:199
↓ 1 callersFunctiongenerate_inference_command
(dataset_name_or_id: Union[int, str], configuration_name: str, plans_identifier
weak_segmentation/nnunetv2/evaluation/find_best_configuration.py:51
↓ 1 callersFunctiongenerate_overlays_from_preprocessed
(dataset_name_or_id: Union[int, str], output_folder: str, num_processe
weak_segmentation/nnunetv2/utilities/overlay_plots.py:209
↓ 1 callersFunctiongenerate_overlays_from_raw
(dataset_name_or_id: Union[int, str], output_folder: str, num_processes: int =
weak_segmentation/nnunetv2/utilities/overlay_plots.py:189
↓ 1 callersFunctiongenerate_readme
(model_card: dict, model_name: str)
biomedclip_finetuning/open_clip/src/open_clip/push_to_hf_hub.py:209
↓ 1 callersFunctiongenerate_shades_with_alpha
(scores, min_alpha=0, max_alpha=0.8)
saliency_maps/scripts/plot.py:38
↓ 1 callersFunctionget_2d_sincos_pos_embed
grid_size: int of the grid height and width return: pos_embed: [grid_size*grid_size, embed_dim] or [1+grid_size*grid_size, embed_dim] (w/
biomedclip_finetuning/open_clip/src/open_clip/pos_embed.py:20
↓ 1 callersFunctionget_2d_sincos_pos_embed_from_grid
(embed_dim, grid)
biomedclip_finetuning/open_clip/src/open_clip/pos_embed.py:38
↓ 1 callersFunctionget_amg_kwargs
(args)
segment-anything/scripts/amg.py:186
↓ 1 callersMethodget_checkpoint
(self)
weak_segmentation/nnunetv2/training/logging/nnunet_logger.py:99
↓ 1 callersFunctionget_clip_metrics
(image_features, text_features, logit_scale)
biomedclip_finetuning/open_clip/src/open_clip_train/train.py:360
↓ 1 callersFunctionget_data
(args, preprocess_fns, epoch=0, tokenizer=None)
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:546
↓ 1 callersFunctionget_data_dirs
(make_dir = True)
biomedclip_finetuning/open_clip/tests/util_test.py:99
↓ 1 callersMethodget_dataloaders
(self)
weak_segmentation/nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py:584
↓ 1 callersFunctionget_default_params
(model_name)
biomedclip_finetuning/open_clip/src/open_clip_train/params.py:5
↓ 1 callersFunctionget_final_mask
(predictor,all_random_points, all_input_labels, bounding_boxes, image, args)
segment-anything/prompt_sam.py:221
↓ 1 callersMethodget_ground_truth
(self, device, dtype, num_logits, negative_only=False)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:388
↓ 1 callersFunctionget_labelmanager_class_from_plans
(plans: dict)
weak_segmentation/nnunetv2/utilities/label_handling/label_handling.py:234
↓ 1 callersFunctionget_latest_checkpoint
(path: str, remote : bool)
biomedclip_finetuning/open_clip/src/open_clip_train/main.py:54
↓ 1 callersMethodget_layer
(self)
saliency_maps/scripts/iba.py:50
↓ 1 callersMethodget_logits
(self, image_features, text_features, logit_scale, logit_bias=None)
biomedclip_finetuning/open_clip/src/open_clip/loss.py:394
↓ 1 callersFunctionget_metrics
(image_feat, vmap, text_ids, tmap, model)
saliency_maps/scripts/eval.py:19
↓ 1 callersFunctionget_network_from_plans
we may have to change this in the future to accommodate other plans -> network mappings num_input_channels can differ depending on whether w
weak_segmentation/nnunetv2/utilities/get_network_from_plans.py:9
↓ 1 callersFunctionget_normalization_scheme
If we find the channel_name in channel_name_to_normalization_mapping return the corresponding normalization. If it is not found, use the defa
weak_segmentation/nnunetv2/preprocessing/normalization/map_channel_name_to_normalization.py:15
↓ 1 callersFunctionget_order
(x)
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:349
↓ 1 callersMethodget_params
Get parameters
biomedclip_finetuning/open_clip/src/open_clip/transform.py:116
↓ 1 callersFunctionget_parser
()
postprocessing/postprocess_saliency_maps.py:153
↓ 1 callersMethodget_plain_dataloaders
(self, initial_patch_size: Tuple[int, ...], dim: int)
weak_segmentation/nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py:630
↓ 1 callersFunctionget_prompts
(mask, args)
segment-anything/prompt_sam.py:181
↓ 1 callersFunctionget_reduction_mask_fn
Choose strategy for dropping (masking) tokens to achieve target context length
biomedclip_finetuning/open_clip/src/open_clip/tokenizer.py:390
↓ 1 callersMethodget_reference_weight
(self)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:306
↓ 1 callersFunctionget_shape_must_be_divisible_by
(net_numpool_per_axis)
weak_segmentation/nnunetv2/experiment_planning/experiment_planners/network_topology.py:5
↓ 1 callersMethodget_training_transforms
(patch_size: Union[np.ndarray, Tuple[int]], rotation_for_DA: dict,
weak_segmentation/nnunetv2/training/nnUNetTrainer/nnUNetTrainer.py:662
↓ 1 callersFunctiongroup_by_keys_nothrow
Return function over iterator that groups key, value pairs into samples. :param keys: function that splits the key into key and extension (base_p
biomedclip_finetuning/open_clip/src/open_clip_train/data.py:186
↓ 1 callersFunctionhex_to_rgb
(hex: str)
weak_segmentation/nnunetv2/utilities/overlay_plots.py:47
↓ 1 callersFunctionhyper_opt
(model, processor, tokenizer, text, args)
saliency_maps/generate_saliency_maps.py:72
↓ 1 callersFunctionimage_transform
( image_size: Union[int, Tuple[int, int]], is_train: bool, mean: Optional[Tuple[float,
biomedclip_finetuning/open_clip/src/open_clip/transform.py:274
↓ 1 callersFunctioninference_image
(model, preprocess_val, batches)
biomedclip_finetuning/open_clip/tests/util_test.py:29
↓ 1 callersFunctioninference_text
(model, model_name, batches)
biomedclip_finetuning/open_clip/tests/util_test.py:20
↓ 1 callersFunctioninit_distributed_device
(args)
biomedclip_finetuning/open_clip/src/open_clip_train/distributed.py:93
↓ 1 callersFunctioninit_distributed_device_so
( device: str = 'cuda', dist_backend: Optional[str] = None, dist_url: Optional[str] =
biomedclip_finetuning/open_clip/src/open_clip_train/distributed.py:116
↓ 1 callersMethodinit_parameters
(self)
biomedclip_finetuning/open_clip/src/open_clip/modified_resnet.py:141
↓ 1 callersMethodinit_parameters
(self)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:574
↓ 1 callersMethodinit_parameters
(self)
biomedclip_finetuning/open_clip/src/open_clip/transformer.py:735
↓ 1 callersFunctionis_box_near_crop_edge
Filter masks at the edge of a crop, but not at the edge of the original image.
segment-anything/segment_anything/utils/amg.py:78
↓ 1 callersFunctionis_device_available
(device)
biomedclip_finetuning/open_clip/src/open_clip_train/distributed.py:26
↓ 1 callersFunctionis_global_master
(args)
biomedclip_finetuning/open_clip/src/open_clip_train/distributed.py:14
↓ 1 callersFunctionis_local_master
(args)
biomedclip_finetuning/open_clip/src/open_clip_train/distributed.py:18
↓ 1 callersFunctionis_using_distributed
()
biomedclip_finetuning/open_clip/src/open_clip_train/distributed.py:65
↓ 1 callersMethodlabel_manager_class
(self)
weak_segmentation/nnunetv2/utilities/plans_handling/plans_handler.py:278
↓ 1 callersFunctionlabels_to_list_of_regions
(labels: List[int])
weak_segmentation/nnunetv2/evaluation/evaluate_predictions.py:63
↓ 1 callersFunctionlist_models
enumerate available model architectures based on config files
biomedclip_finetuning/open_clip/src/open_clip/factory.py:56
↓ 1 callersFunctionlist_openai_models
Returns the names of available CLIP models
biomedclip_finetuning/open_clip/src/open_clip/openai.py:19
↓ 1 callersFunctionlist_pretrained_models_by_tag
return all models having the specified pretrain tag
biomedclip_finetuning/open_clip/src/open_clip/pretrained.py:618
↓ 1 callersFunctionlist_pretrained_tags_by_model
return all pretrain tags for the specified model architecture
biomedclip_finetuning/open_clip/src/open_clip/pretrained.py:628
↓ 1 callersFunctionload_big_vision_weights
Load weights from .npz checkpoints for official Google big_vision image-text models Currently the SigLIP source models are supported and a Custo
biomedclip_finetuning/open_clip/src/open_clip/convert.py:13
↓ 1 callersMethodload_checkpoint
(self, checkpoint: dict)
weak_segmentation/nnunetv2/training/logging/nnunet_logger.py:102
↓ 1 callersFunctionload_pretrained_weights
Transfers all weights between matching keys in state_dicts. matching is done by name and we only transfer if the shape is also the same. Segm
weak_segmentation/nnunetv2/run/load_pretrained_weights.py:6
↓ 1 callersFunctionload_state_dict
( checkpoint_path: str, device='cpu', weights_only=True, )
biomedclip_finetuning/open_clip/src/open_clip/factory.py:141
↓ 1 callersMethodlock_image_tower
(self, unlocked_groups=0, freeze_bn_stats=False)
biomedclip_finetuning/open_clip/src/open_clip/model.py:258
↓ 1 callersMethodlock_text_tower
(self, unlocked_layers: int = 0, freeze_layer_norm: bool = True)
biomedclip_finetuning/open_clip/src/open_clip/model.py:350
↓ 1 callersFunctionmain
(args: argparse.Namespace)
segment-anything/prompt_sam.py:291
↓ 1 callersFunctionmain
(args: argparse.Namespace)
segment-anything/scripts/amg.py:204
↓ 1 callersFunctionmain
(args)
saliency_maps/generate_saliency_maps.py:130
↓ 1 callersFunctionmain
(args)
saliency_maps/scripts/eval.py:38
↓ 1 callersFunctionmain
()
biomedclip_finetuning/open_clip/src/open_clip_train/profiler.py:208
↓ 1 callersFunctionmain
(args)
biomedclip_finetuning/open_clip/tests/util_test.py:217
↓ 1 callersFunctionmake_out_dirs
(dataset_id: int, task_name="ACDC")
weak_segmentation/nnunetv2/dataset_conversion/Dataset027_ACDC.py:9
↓ 1 callersMethodmanual_initialization
This is used by the nnUNetTrainer to initialize nnUNetPredictor for the final validation
weak_segmentation/nnunetv2/inference/predict_from_raw_data.py:116
↓ 1 callersMethodmask_postprocessing
(self, masks: torch.Tensor, orig_im_size: torch.Tensor)
segment-anything/segment_anything/utils/onnx.py:76
↓ 1 callersFunctionmaybe_compute_generative_loss
(model_out)
biomedclip_finetuning/open_clip/src/open_clip_train/train.py:380
↓ 1 callersFunctionmerge
(dict1, dict2)
weak_segmentation/nnunetv2/batch_running/generate_lsf_runs_customDecathlon.py:5
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