mmv_im2im package

Subpackages

• mmv_im2im.bin package
  • Submodules
  • mmv_im2im.bin.run_im2im module
    • main()
  • Module contents
• mmv_im2im.configs package
  • Submodules
  • mmv_im2im.configs.config_base module
    • ArgumentParser
      • ArgumentParser.parse_args()
      • ArgumentParser.parse_known_args()
      • ArgumentParser.print_help()
      • ArgumentParser.set_dataclass()
    • DataConfig
      • DataConfig.augmentation
      • DataConfig.cache_path
      • DataConfig.category
      • DataConfig.data_path
      • DataConfig.dataloader
      • DataConfig.extra
      • DataConfig.inference_input
      • DataConfig.inference_output
      • DataConfig.patch_size
      • DataConfig.postprocess
      • DataConfig.preprocess
    • DataloaderConfig
      • DataloaderConfig.train
      • DataloaderConfig.train_val_ratio
      • DataloaderConfig.val
    • DataloaderModuleConfig
      • DataloaderModuleConfig.dataloader_params
      • DataloaderModuleConfig.dataloader_type
      • DataloaderModuleConfig.dataset_params
      • DataloaderModuleConfig.partial_loader
    • InferInConfig
      • InferInConfig.data_type
      • InferInConfig.dir
      • InferInConfig.reader_params
    • InferOutConfig
      • InferOutConfig.path
      • InferOutConfig.suffix
    • ModelConfig
      • ModelConfig.checkpoint
      • ModelConfig.criterion
      • ModelConfig.framework
      • ModelConfig.model_extra
      • ModelConfig.net
      • ModelConfig.optimizer
      • ModelConfig.scheduler
    • ProgramConfig
      • ProgramConfig.data
      • ProgramConfig.mode
      • ProgramConfig.model
      • ProgramConfig.trainer
    • TrainerConfig
      • TrainerConfig.callbacks
      • TrainerConfig.gpus
      • TrainerConfig.params
      • TrainerConfig.verbose
    • configuration_validation()
    • parse_adaptor()
  • Module contents
• mmv_im2im.data_modules package
  • Submodules
  • mmv_im2im.data_modules.data_loader_basic module
    • Im2ImDataModule
      • Im2ImDataModule.prepare_data()
      • Im2ImDataModule.setup()
      • Im2ImDataModule.train_dataloader()
      • Im2ImDataModule.val_dataloader()
  • Module contents
    • get_data_module()
• mmv_im2im.models package
  • Subpackages
    • mmv_im2im.models.nets package
      • Submodules
      • mmv_im2im.models.nets.BranchedERFNet_2d module
      • mmv_im2im.models.nets.BranchedERFNet_3d module
      • mmv_im2im.models.nets.SA_2d 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
      • Module contents
  • Submodules
  • mmv_im2im.models.pl_FCN module
    • Model
      • Model.configure_optimizers()
      • Model.forward()
      • Model.prepare_batch()
      • Model.run_step()
      • Model.training_epoch_end()
      • Model.training_step()
      • Model.validation_epoch_end()
      • Model.validation_step()
  • mmv_im2im.models.pl_cyclegan module
    • Model
      • Model.configure_optimizers()
      • Model.forward()
      • Model.run_step()
      • Model.save_cyclegan_output()
      • Model.training_epoch_end()
      • Model.training_step()
      • Model.validation_epoch_end()
      • Model.validation_step()
  • mmv_im2im.models.pl_embedseg module
    • Model
      • Model.configure_optimizers()
      • Model.forward()
      • Model.run_step()
      • Model.training_epoch_end()
      • Model.training_step()
      • Model.validation_epoch_end()
      • Model.validation_step()
  • mmv_im2im.models.pl_pix2pix module
    • Model
      • Model.configure_optimizers()
      • Model.forward()
      • Model.save_pix2pix_output()
      • Model.training_epoch_end()
      • Model.training_step()
      • Model.validation_epoch_end()
      • Model.validation_step()
  • Module contents
• mmv_im2im.postprocessing package
  • Submodules
  • mmv_im2im.postprocessing.basic_collection module
    • extract_segmentation()
    • generate_classmap()
  • mmv_im2im.postprocessing.embedseg_cluster module
    • Cluster_2d
      • Cluster_2d.cluster()
      • Cluster_2d.cluster_with_gt()
    • Cluster_3d
      • Cluster_3d.cluster()
      • Cluster_3d.cluster_with_gt()
    • degrid()
    • generate_instance_clusters()
  • Module contents
• mmv_im2im.preprocessing package
  • Submodules
  • mmv_im2im.preprocessing.transforms module
    • norm_around_center()
    • normalize_staining()
    • pad_to_multiple()
    • pad_z()
  • Module contents
• mmv_im2im.utils package
  • Submodules
  • mmv_im2im.utils.basic_losses module
    • PixelWiseCrossEntropyLoss
      • PixelWiseCrossEntropyLoss.forward()
      • PixelWiseCrossEntropyLoss.training
    • expand_as_one_hot()
  • mmv_im2im.utils.embedding_loss module
    • SpatialEmbLoss_2d
      • SpatialEmbLoss_2d.forward()
      • SpatialEmbLoss_2d.training
    • SpatialEmbLoss_3d
      • SpatialEmbLoss_3d.forward()
      • SpatialEmbLoss_3d.training
    • calculate_iou()
  • mmv_im2im.utils.embedseg_utils module
    • fill_label_holes()
    • generate_center_image()
    • generate_center_image_2d()
    • generate_center_image_3d()
    • pairwise_python()
    • prepare_embedseg_cache()
    • prepare_embedseg_tensor()
  • mmv_im2im.utils.for_transform module
    • center_crop()
    • parse_monai_ops()
    • parse_monai_ops_vanilla()
  • mmv_im2im.utils.gan_losses module
    • pix2pix_HD
      • pix2pix_HD.generator_step()
    • pix2pix_HD_original
      • pix2pix_HD_original.discriminator_step()
      • pix2pix_HD_original.feature_matching()
      • pix2pix_HD_original.generator_step()
      • pix2pix_HD_original.multi_gan()
    • pix2pix_basic
      • pix2pix_basic.discriminator_step()
      • pix2pix_basic.generator_step()
  • mmv_im2im.utils.gan_utils module
    • ReplayBuffer
      • ReplayBuffer.push_and_pop()
  • mmv_im2im.utils.lovasz_losses module
    • StableBCELoss
      • StableBCELoss.forward()
      • StableBCELoss.training
    • binary_xloss()
    • flatten_binary_scores()
    • flatten_probas()
    • iou()
    • iou_binary()
    • lovasz_grad()
    • lovasz_hinge()
    • lovasz_hinge_flat()
    • lovasz_softmax()
    • lovasz_softmax_flat()
    • mean()
    • xloss()
  • mmv_im2im.utils.metrics module
    • simplified_instance_IoU_3D()
  • mmv_im2im.utils.misc module
    • generate_dataset_dict()
    • generate_dataset_dict_monai()
    • generate_test_dataset_dict()
    • load_one_folder()
    • load_subfolders()
    • monai_bio_reader
      • monai_bio_reader.get_data()
      • monai_bio_reader.read()
      • monai_bio_reader.verify_suffix()
    • parse_config()
    • parse_config_func()
    • parse_config_func_without_params()
    • parse_ops_list()
  • mmv_im2im.utils.model_utils module
    • init_weights()
    • state_dict_simplification()
  • Module contents

Submodules

mmv_im2im.proj_tester module

class mmv_im2im.proj_tester.ProjectTester(cfg)

Bases: object

entry for training models

Parameters:

cfg (configuration)

process_one_image(img: Array | ndarray, out_fn: str | Path | None = None)

run_inference()

setup_data_processing()

setup_model()

mmv_im2im.proj_trainer module

class mmv_im2im.proj_trainer.ProjectTrainer(cfg)

Bases: object

entry for training models

Parameters:

cfg (configuration)

run_training()

Module contents

Top-level package for MMV Im2Im Transformation.

mmv_im2im.get_module_version()