Index

A

ArgumentParser (class in mmv_im2im.configs.config_base)

augmentation (mmv_im2im.configs.config_base.DataConfig attribute)

B

binary_xloss() (in module mmv_im2im.utils.lovasz_losses) Bottleneck (class in mmv_im2im.models.nets.SA_2d)

Bottleneck_transition (class in mmv_im2im.models.nets.SA_2d) BranchedERFNet_2d (class in mmv_im2im.models.nets.BranchedERFNet_2d) BranchedERFNet_3d (class in mmv_im2im.models.nets.BranchedERFNet_3d)

C

cache_path (mmv_im2im.configs.config_base.DataConfig attribute) calculate_iou() (in module mmv_im2im.utils.embedding_loss) callbacks (mmv_im2im.configs.config_base.TrainerConfig attribute) category (mmv_im2im.configs.config_base.DataConfig attribute) center_crop() (in module mmv_im2im.utils.for_transform) checkpoint (mmv_im2im.configs.config_base.ModelConfig attribute) cluster() (mmv_im2im.postprocessing.embedseg_cluster.Cluster_2d method) (mmv_im2im.postprocessing.embedseg_cluster.Cluster_3d method) Cluster_2d (class in mmv_im2im.postprocessing.embedseg_cluster)

Cluster_3d (class in mmv_im2im.postprocessing.embedseg_cluster) cluster_with_gt() (mmv_im2im.postprocessing.embedseg_cluster.Cluster_2d method) (mmv_im2im.postprocessing.embedseg_cluster.Cluster_3d method) configuration_validation() (in module mmv_im2im.configs.config_base) configure_optimizers() (mmv_im2im.models.pl_cyclegan.Model method) (mmv_im2im.models.pl_embedseg.Model method) (mmv_im2im.models.pl_FCN.Model method) (mmv_im2im.models.pl_pix2pix.Model method) criterion (mmv_im2im.configs.config_base.ModelConfig attribute)

D

data (mmv_im2im.configs.config_base.ProgramConfig attribute) data_path (mmv_im2im.configs.config_base.DataConfig attribute) data_type (mmv_im2im.configs.config_base.InferInConfig attribute) DataConfig (class in mmv_im2im.configs.config_base) dataloader (mmv_im2im.configs.config_base.DataConfig attribute) dataloader_params (mmv_im2im.configs.config_base.DataloaderModuleConfig attribute) dataloader_type (mmv_im2im.configs.config_base.DataloaderModuleConfig attribute) DataloaderConfig (class in mmv_im2im.configs.config_base) DataloaderModuleConfig (class in mmv_im2im.configs.config_base) dataset_params (mmv_im2im.configs.config_base.DataloaderModuleConfig attribute)

Decoder (class in mmv_im2im.models.nets.erfnet) (class in mmv_im2im.models.nets.erfnet_3d) define_discriminator() (in module mmv_im2im.models.nets.gans) define_generator() (in module mmv_im2im.models.nets.gans) degrid() (in module mmv_im2im.postprocessing.embedseg_cluster) dir (mmv_im2im.configs.config_base.InferInConfig attribute) discriminator_step() (mmv_im2im.utils.gan_losses.pix2pix_basic method) (mmv_im2im.utils.gan_losses.pix2pix_HD_original method) DownsamplerBlock (class in mmv_im2im.models.nets.erfnet) (class in mmv_im2im.models.nets.erfnet_3d)

E

Encoder (class in mmv_im2im.models.nets.erfnet) (class in mmv_im2im.models.nets.erfnet_3d)

expand_as_one_hot() (in module mmv_im2im.utils.basic_losses) extra (mmv_im2im.configs.config_base.DataConfig attribute) extract_segmentation() (in module mmv_im2im.postprocessing.basic_collection)

F

feature_matching() (mmv_im2im.utils.gan_losses.pix2pix_HD_original method) fill_label_holes() (in module mmv_im2im.utils.embedseg_utils) flatten_binary_scores() (in module mmv_im2im.utils.lovasz_losses) flatten_probas() (in module mmv_im2im.utils.lovasz_losses) forward() (mmv_im2im.models.nets.BranchedERFNet_2d.BranchedERFNet_2d method) (mmv_im2im.models.nets.BranchedERFNet_3d.BranchedERFNet_3d method) (mmv_im2im.models.nets.deeplabv3_2d.Net method) (mmv_im2im.models.nets.erfnet.Decoder method) (mmv_im2im.models.nets.erfnet.DownsamplerBlock method) (mmv_im2im.models.nets.erfnet.Encoder method) (mmv_im2im.models.nets.erfnet.Net method) (mmv_im2im.models.nets.erfnet.non_bottleneck_1d method) (mmv_im2im.models.nets.erfnet.UpsamplerBlock method) (mmv_im2im.models.nets.erfnet_3d.Decoder method) (mmv_im2im.models.nets.erfnet_3d.DownsamplerBlock method) (mmv_im2im.models.nets.erfnet_3d.Encoder method) (mmv_im2im.models.nets.erfnet_3d.Net method) (mmv_im2im.models.nets.erfnet_3d.non_bottleneck_1d method) (mmv_im2im.models.nets.erfnet_3d.UpsamplerBlock method) (mmv_im2im.models.nets.fnet_nn_2d.Net method) (mmv_im2im.models.nets.fnet_nn_2d.SubNet2Conv method) (mmv_im2im.models.nets.fnet_nn_3d.Net method) (mmv_im2im.models.nets.fnet_nn_3d.SubNet2Conv method) (mmv_im2im.models.nets.gans.generator_encoder_decoder method) (mmv_im2im.models.nets.gans.multiscale_discriminator method) (mmv_im2im.models.nets.gans.patch_discriminator method) (mmv_im2im.models.nets.gans.preset_generator_resent method) (mmv_im2im.models.nets.SA_2d.Bottleneck method) (mmv_im2im.models.nets.SA_2d.Bottleneck_transition method) (mmv_im2im.models.nets.SA_2d.SuggestiveAnnotationModel method) (mmv_im2im.models.pl_cyclegan.Model method) (mmv_im2im.models.pl_embedseg.Model method) (mmv_im2im.models.pl_FCN.Model method) (mmv_im2im.models.pl_pix2pix.Model method) (mmv_im2im.utils.basic_losses.PixelWiseCrossEntropyLoss method) (mmv_im2im.utils.embedding_loss.SpatialEmbLoss_2d method) (mmv_im2im.utils.embedding_loss.SpatialEmbLoss_3d method) (mmv_im2im.utils.lovasz_losses.StableBCELoss method)

framework (mmv_im2im.configs.config_base.ModelConfig attribute)

G

generate_center_image() (in module mmv_im2im.utils.embedseg_utils) generate_center_image_2d() (in module mmv_im2im.utils.embedseg_utils) generate_center_image_3d() (in module mmv_im2im.utils.embedseg_utils) generate_classmap() (in module mmv_im2im.postprocessing.basic_collection) generate_dataset_dict() (in module mmv_im2im.utils.misc) generate_dataset_dict_monai() (in module mmv_im2im.utils.misc) generate_instance_clusters() (in module mmv_im2im.postprocessing.embedseg_cluster) generate_test_dataset_dict() (in module mmv_im2im.utils.misc)

generator_encoder_decoder (class in mmv_im2im.models.nets.gans) generator_step() (mmv_im2im.utils.gan_losses.pix2pix_basic method) (mmv_im2im.utils.gan_losses.pix2pix_HD method) (mmv_im2im.utils.gan_losses.pix2pix_HD_original method) get_data() (mmv_im2im.utils.misc.monai_bio_reader method) get_data_module() (in module mmv_im2im.data_modules) get_module_version() (in module mmv_im2im) gpus (mmv_im2im.configs.config_base.TrainerConfig attribute)

I

Im2ImDataModule (class in mmv_im2im.data_modules.data_loader_basic) inference_input (mmv_im2im.configs.config_base.DataConfig attribute) inference_output (mmv_im2im.configs.config_base.DataConfig attribute) InferInConfig (class in mmv_im2im.configs.config_base) InferOutConfig (class in mmv_im2im.configs.config_base)

init_output() (mmv_im2im.models.nets.BranchedERFNet_2d.BranchedERFNet_2d method) (mmv_im2im.models.nets.BranchedERFNet_3d.BranchedERFNet_3d method) init_weights() (in module mmv_im2im.utils.model_utils) iou() (in module mmv_im2im.utils.lovasz_losses) iou_binary() (in module mmv_im2im.utils.lovasz_losses)

L

load_one_folder() (in module mmv_im2im.utils.misc) load_subfolders() (in module mmv_im2im.utils.misc) lovasz_grad() (in module mmv_im2im.utils.lovasz_losses)

lovasz_hinge() (in module mmv_im2im.utils.lovasz_losses) lovasz_hinge_flat() (in module mmv_im2im.utils.lovasz_losses) lovasz_softmax() (in module mmv_im2im.utils.lovasz_losses) lovasz_softmax_flat() (in module mmv_im2im.utils.lovasz_losses)

M

main() (in module mmv_im2im.bin.run_im2im) mean() (in module mmv_im2im.utils.lovasz_losses) mmv_im2im module mmv_im2im.bin module mmv_im2im.bin.run_im2im module mmv_im2im.configs module mmv_im2im.configs.config_base module mmv_im2im.data_modules module mmv_im2im.data_modules.data_loader_basic module mmv_im2im.models module mmv_im2im.models.nets module mmv_im2im.models.nets.BranchedERFNet_2d module mmv_im2im.models.nets.BranchedERFNet_3d module mmv_im2im.models.nets.deeplabv3_2d module mmv_im2im.models.nets.erfnet module mmv_im2im.models.nets.erfnet_3d module mmv_im2im.models.nets.fnet_nn_2d module mmv_im2im.models.nets.fnet_nn_3d module mmv_im2im.models.nets.gans module mmv_im2im.models.nets.SA_2d module mmv_im2im.models.pl_cyclegan module mmv_im2im.models.pl_embedseg module mmv_im2im.models.pl_FCN module mmv_im2im.models.pl_pix2pix module mmv_im2im.postprocessing module mmv_im2im.postprocessing.basic_collection module mmv_im2im.postprocessing.embedseg_cluster module mmv_im2im.preprocessing module mmv_im2im.preprocessing.transforms module mmv_im2im.proj_tester module mmv_im2im.proj_trainer module mmv_im2im.utils module mmv_im2im.utils.basic_losses module mmv_im2im.utils.embedding_loss module mmv_im2im.utils.embedseg_utils module

mmv_im2im.utils.for_transform module mmv_im2im.utils.gan_losses module mmv_im2im.utils.gan_utils module mmv_im2im.utils.lovasz_losses module mmv_im2im.utils.metrics module mmv_im2im.utils.misc module mmv_im2im.utils.model_utils module mode (mmv_im2im.configs.config_base.ProgramConfig attribute) Model (class in mmv_im2im.models.pl_cyclegan) (class in mmv_im2im.models.pl_embedseg) (class in mmv_im2im.models.pl_FCN) (class in mmv_im2im.models.pl_pix2pix) model (mmv_im2im.configs.config_base.ProgramConfig attribute) model_extra (mmv_im2im.configs.config_base.ModelConfig attribute) ModelConfig (class in mmv_im2im.configs.config_base) module mmv_im2im mmv_im2im.bin mmv_im2im.bin.run_im2im mmv_im2im.configs mmv_im2im.configs.config_base mmv_im2im.data_modules mmv_im2im.data_modules.data_loader_basic mmv_im2im.models mmv_im2im.models.nets mmv_im2im.models.nets.BranchedERFNet_2d mmv_im2im.models.nets.BranchedERFNet_3d mmv_im2im.models.nets.deeplabv3_2d mmv_im2im.models.nets.erfnet mmv_im2im.models.nets.erfnet_3d mmv_im2im.models.nets.fnet_nn_2d mmv_im2im.models.nets.fnet_nn_3d mmv_im2im.models.nets.gans mmv_im2im.models.nets.SA_2d mmv_im2im.models.pl_cyclegan mmv_im2im.models.pl_embedseg mmv_im2im.models.pl_FCN mmv_im2im.models.pl_pix2pix mmv_im2im.postprocessing mmv_im2im.postprocessing.basic_collection mmv_im2im.postprocessing.embedseg_cluster mmv_im2im.preprocessing mmv_im2im.preprocessing.transforms mmv_im2im.proj_tester mmv_im2im.proj_trainer mmv_im2im.utils mmv_im2im.utils.basic_losses mmv_im2im.utils.embedding_loss mmv_im2im.utils.embedseg_utils mmv_im2im.utils.for_transform mmv_im2im.utils.gan_losses mmv_im2im.utils.gan_utils mmv_im2im.utils.lovasz_losses mmv_im2im.utils.metrics mmv_im2im.utils.misc mmv_im2im.utils.model_utils monai_bio_reader (class in mmv_im2im.utils.misc) multi_gan() (mmv_im2im.utils.gan_losses.pix2pix_HD_original method) multiscale_discriminator (class in mmv_im2im.models.nets.gans)

N

Net (class in mmv_im2im.models.nets.deeplabv3_2d) (class in mmv_im2im.models.nets.erfnet) (class in mmv_im2im.models.nets.erfnet_3d) (class in mmv_im2im.models.nets.fnet_nn_2d) (class in mmv_im2im.models.nets.fnet_nn_3d)

net (mmv_im2im.configs.config_base.ModelConfig attribute) non_bottleneck_1d (class in mmv_im2im.models.nets.erfnet) (class in mmv_im2im.models.nets.erfnet_3d) norm_around_center() (in module mmv_im2im.preprocessing.transforms) normalize_staining() (in module mmv_im2im.preprocessing.transforms)

O

optimizer (mmv_im2im.configs.config_base.ModelConfig attribute)

P

pad_to_multiple() (in module mmv_im2im.preprocessing.transforms) pad_z() (in module mmv_im2im.preprocessing.transforms) pairwise_python() (in module mmv_im2im.utils.embedseg_utils) params (mmv_im2im.configs.config_base.TrainerConfig attribute) parse_adaptor() (in module mmv_im2im.configs.config_base) parse_args() (mmv_im2im.configs.config_base.ArgumentParser method) parse_config() (in module mmv_im2im.utils.misc) parse_config_func() (in module mmv_im2im.utils.misc) parse_config_func_without_params() (in module mmv_im2im.utils.misc) parse_known_args() (mmv_im2im.configs.config_base.ArgumentParser method) parse_monai_ops() (in module mmv_im2im.utils.for_transform) parse_monai_ops_vanilla() (in module mmv_im2im.utils.for_transform) parse_ops_list() (in module mmv_im2im.utils.misc) partial_loader (mmv_im2im.configs.config_base.DataloaderModuleConfig attribute) patch_discriminator (class in mmv_im2im.models.nets.gans) patch_size (mmv_im2im.configs.config_base.DataConfig attribute) path (mmv_im2im.configs.config_base.InferOutConfig attribute)

pix2pix_basic (class in mmv_im2im.utils.gan_losses) pix2pix_HD (class in mmv_im2im.utils.gan_losses) pix2pix_HD_original (class in mmv_im2im.utils.gan_losses) PixelWiseCrossEntropyLoss (class in mmv_im2im.utils.basic_losses) postprocess (mmv_im2im.configs.config_base.DataConfig attribute) prepare_batch() (mmv_im2im.models.pl_FCN.Model method) prepare_data() (mmv_im2im.data_modules.data_loader_basic.Im2ImDataModule method) prepare_embedseg_cache() (in module mmv_im2im.utils.embedseg_utils) prepare_embedseg_tensor() (in module mmv_im2im.utils.embedseg_utils) preprocess (mmv_im2im.configs.config_base.DataConfig attribute) preset_generator_resent (class in mmv_im2im.models.nets.gans) print_help() (mmv_im2im.configs.config_base.ArgumentParser method) process_one_image() (mmv_im2im.proj_tester.ProjectTester method) ProgramConfig (class in mmv_im2im.configs.config_base) ProjectTester (class in mmv_im2im.proj_tester) ProjectTrainer (class in mmv_im2im.proj_trainer) push_and_pop() (mmv_im2im.utils.gan_utils.ReplayBuffer method)

R

read() (mmv_im2im.utils.misc.monai_bio_reader method) reader_params (mmv_im2im.configs.config_base.InferInConfig attribute) ReplayBuffer (class in mmv_im2im.utils.gan_utils) run_inference() (mmv_im2im.proj_tester.ProjectTester method)

run_step() (mmv_im2im.models.pl_cyclegan.Model method) (mmv_im2im.models.pl_embedseg.Model method) (mmv_im2im.models.pl_FCN.Model method) run_training() (mmv_im2im.proj_trainer.ProjectTrainer method)

S

save_cyclegan_output() (mmv_im2im.models.pl_cyclegan.Model method) save_pix2pix_output() (mmv_im2im.models.pl_pix2pix.Model method) scheduler (mmv_im2im.configs.config_base.ModelConfig attribute) set_dataclass() (mmv_im2im.configs.config_base.ArgumentParser method) setup() (mmv_im2im.data_modules.data_loader_basic.Im2ImDataModule method) setup_data_processing() (mmv_im2im.proj_tester.ProjectTester method) setup_model() (mmv_im2im.proj_tester.ProjectTester method) simplified_instance_IoU_3D() (in module mmv_im2im.utils.metrics)

SpatialEmbLoss_2d (class in mmv_im2im.utils.embedding_loss) SpatialEmbLoss_3d (class in mmv_im2im.utils.embedding_loss) StableBCELoss (class in mmv_im2im.utils.lovasz_losses) state_dict_simplification() (in module mmv_im2im.utils.model_utils) SubNet2Conv (class in mmv_im2im.models.nets.fnet_nn_2d) (class in mmv_im2im.models.nets.fnet_nn_3d) suffix (mmv_im2im.configs.config_base.InferOutConfig attribute) SuggestiveAnnotationModel (class in mmv_im2im.models.nets.SA_2d)

T

train (mmv_im2im.configs.config_base.DataloaderConfig attribute) train_dataloader() (mmv_im2im.data_modules.data_loader_basic.Im2ImDataModule method) train_val_ratio (mmv_im2im.configs.config_base.DataloaderConfig attribute) trainer (mmv_im2im.configs.config_base.ProgramConfig attribute) TrainerConfig (class in mmv_im2im.configs.config_base) training (mmv_im2im.models.nets.BranchedERFNet_2d.BranchedERFNet_2d attribute) (mmv_im2im.models.nets.BranchedERFNet_3d.BranchedERFNet_3d attribute) (mmv_im2im.models.nets.deeplabv3_2d.Net attribute) (mmv_im2im.models.nets.erfnet.Decoder attribute) (mmv_im2im.models.nets.erfnet.DownsamplerBlock attribute) (mmv_im2im.models.nets.erfnet.Encoder attribute) (mmv_im2im.models.nets.erfnet.Net attribute) (mmv_im2im.models.nets.erfnet.non_bottleneck_1d attribute) (mmv_im2im.models.nets.erfnet.UpsamplerBlock attribute) (mmv_im2im.models.nets.erfnet_3d.Decoder attribute) (mmv_im2im.models.nets.erfnet_3d.DownsamplerBlock attribute) (mmv_im2im.models.nets.erfnet_3d.Encoder attribute) (mmv_im2im.models.nets.erfnet_3d.Net attribute) (mmv_im2im.models.nets.erfnet_3d.non_bottleneck_1d attribute) (mmv_im2im.models.nets.erfnet_3d.UpsamplerBlock attribute) (mmv_im2im.models.nets.fnet_nn_2d.Net attribute) (mmv_im2im.models.nets.fnet_nn_2d.SubNet2Conv attribute) (mmv_im2im.models.nets.fnet_nn_3d.Net attribute) (mmv_im2im.models.nets.fnet_nn_3d.SubNet2Conv attribute) (mmv_im2im.models.nets.gans.generator_encoder_decoder attribute) (mmv_im2im.models.nets.gans.multiscale_discriminator attribute) (mmv_im2im.models.nets.gans.patch_discriminator attribute) (mmv_im2im.models.nets.gans.preset_generator_resent attribute) (mmv_im2im.models.nets.SA_2d.Bottleneck attribute) (mmv_im2im.models.nets.SA_2d.Bottleneck_transition attribute) (mmv_im2im.models.nets.SA_2d.SuggestiveAnnotationModel attribute) (mmv_im2im.utils.basic_losses.PixelWiseCrossEntropyLoss attribute) (mmv_im2im.utils.embedding_loss.SpatialEmbLoss_2d attribute) (mmv_im2im.utils.embedding_loss.SpatialEmbLoss_3d attribute) (mmv_im2im.utils.lovasz_losses.StableBCELoss attribute)

training_epoch_end() (mmv_im2im.models.pl_cyclegan.Model method) (mmv_im2im.models.pl_embedseg.Model method) (mmv_im2im.models.pl_FCN.Model method) (mmv_im2im.models.pl_pix2pix.Model method) training_step() (mmv_im2im.models.pl_cyclegan.Model method) (mmv_im2im.models.pl_embedseg.Model method) (mmv_im2im.models.pl_FCN.Model method) (mmv_im2im.models.pl_pix2pix.Model method)

U

UpsamplerBlock (class in mmv_im2im.models.nets.erfnet) (class in mmv_im2im.models.nets.erfnet_3d)

V

val (mmv_im2im.configs.config_base.DataloaderConfig attribute) val_dataloader() (mmv_im2im.data_modules.data_loader_basic.Im2ImDataModule method) validation_epoch_end() (mmv_im2im.models.pl_cyclegan.Model method) (mmv_im2im.models.pl_embedseg.Model method) (mmv_im2im.models.pl_FCN.Model method) (mmv_im2im.models.pl_pix2pix.Model method)

validation_step() (mmv_im2im.models.pl_cyclegan.Model method) (mmv_im2im.models.pl_embedseg.Model method) (mmv_im2im.models.pl_FCN.Model method) (mmv_im2im.models.pl_pix2pix.Model method) verbose (mmv_im2im.configs.config_base.TrainerConfig attribute) verify_suffix() (mmv_im2im.utils.misc.monai_bio_reader method)

X

xloss() (in module mmv_im2im.utils.lovasz_losses)