pymic package

Subpackages

• pymic.io package
  • Submodules
  • pymic.io.h5_dataset module
    • H5DataSet
    • TwoStreamBatchSampler
    • grouper()
    • iterate_eternally()
    • iterate_once()
  • pymic.io.image_read_write module
    • load_image_as_nd_array()
    • load_nifty_volume_as_4d_array()
    • load_rgb_image_as_3d_array()
    • rotate_nifty_volume_to_LPS()
    • save_array_as_nifty_volume()
    • save_array_as_rgb_image()
    • save_nd_array_as_image()
  • pymic.io.nifty_dataset module
    • ClassificationDataset
    • NiftyDataset
  • Module contents
• pymic.layer package
  • Submodules
  • pymic.layer.activation module
    • get_acti_func()
  • pymic.layer.convolution module
    • ConvolutionLayer
      • ConvolutionLayer.forward()
      • ConvolutionLayer.training
    • DepthSeperableConvolutionLayer
      • DepthSeperableConvolutionLayer.forward()
      • DepthSeperableConvolutionLayer.training
  • pymic.layer.deconvolution module
    • DeconvolutionLayer
      • DeconvolutionLayer.forward()
      • DeconvolutionLayer.training
    • DepthSeperableDeconvolutionLayer
      • DepthSeperableDeconvolutionLayer.forward()
      • DepthSeperableDeconvolutionLayer.training
  • pymic.layer.space2channel module
    • ChannelToSpace3D
      • ChannelToSpace3D.forward()
      • ChannelToSpace3D.training
    • SpaceToChannel3D
      • SpaceToChannel3D.forward()
      • SpaceToChannel3D.training
  • Module contents
• pymic.loss package
  • Subpackages
    • pymic.loss.cls package
      • Submodules
      • pymic.loss.cls.basic module
      • pymic.loss.cls.util module
      • Module contents
    • pymic.loss.seg package
      • Submodules
      • pymic.loss.seg.abstract module
      • pymic.loss.seg.ce module
      • pymic.loss.seg.combined module
      • pymic.loss.seg.deep_sup module
      • pymic.loss.seg.dice module
      • pymic.loss.seg.exp_log module
      • pymic.loss.seg.gatedcrf module
      • pymic.loss.seg.mse module
      • pymic.loss.seg.mumford_shah module
      • pymic.loss.seg.slsr module
      • pymic.loss.seg.ssl module
      • pymic.loss.seg.util module
      • Module contents
  • Submodules
  • pymic.loss.loss_dict_cls module
  • pymic.loss.loss_dict_seg module
  • Module contents
• pymic.net package
  • Subpackages
    • pymic.net.cls package
      • Submodules
      • pymic.net.cls.torch_pretrained_net module
      • Module contents
    • pymic.net.net2d package
      • Submodules
      • pymic.net.net2d.cople_net module
      • pymic.net.net2d.scse2d module
      • pymic.net.net2d.unet2d module
      • pymic.net.net2d.unet2d_attention module
      • pymic.net.net2d.unet2d_cct module
      • pymic.net.net2d.unet2d_dual_branch module
      • pymic.net.net2d.unet2d_nest module
      • pymic.net.net2d.unet2d_scse module
      • pymic.net.net2d.unet2d_urpc module
      • Module contents
    • pymic.net.net3d package
      • Submodules
      • pymic.net.net3d.scse3d module
      • pymic.net.net3d.unet2d5 module
      • pymic.net.net3d.unet3d module
      • pymic.net.net3d.unet3d_scse module
      • Module contents
  • Submodules
  • pymic.net.net_dict_cls module
  • pymic.net.net_dict_seg module
  • Module contents
• pymic.net_run package
  • Subpackages
    • pymic.net_run.semi_sup package
      • Submodules
      • pymic.net_run.semi_sup.ssl_abstract module
      • pymic.net_run.semi_sup.ssl_cct module
      • pymic.net_run.semi_sup.ssl_cps module
      • pymic.net_run.semi_sup.ssl_em module
      • pymic.net_run.semi_sup.ssl_mt module
      • pymic.net_run.semi_sup.ssl_uamt module
      • pymic.net_run.semi_sup.ssl_urpc module
      • Module contents
    • pymic.net_run.weak_sup package
      • Submodules
      • pymic.net_run.weak_sup.wsl_abstract module
      • pymic.net_run.weak_sup.wsl_dmpls module
      • pymic.net_run.weak_sup.wsl_em module
      • pymic.net_run.weak_sup.wsl_gatedcrf module
      • pymic.net_run.weak_sup.wsl_mumford_shah module
      • pymic.net_run.weak_sup.wsl_tv module
      • pymic.net_run.weak_sup.wsl_ustm module
      • Module contents
    • pymic.net_run.noisy_label package
      • Submodules
      • pymic.net_run.noisy_label.nll_clslsr module
      • pymic.net_run.noisy_label.nll_co_teaching module
      • pymic.net_run.noisy_label.nll_dast module
      • pymic.net_run.noisy_label.nll_trinet module
      • Module contents
  • Submodules
  • pymic.net_run.agent_abstract module
    • NetRunAgent
      • NetRunAgent.convert_tensor_type()
      • NetRunAgent.create_dataset()
      • NetRunAgent.create_loss_calculator()
      • NetRunAgent.create_network()
      • NetRunAgent.create_optimizer()
      • NetRunAgent.get_checkpoint_name()
      • NetRunAgent.get_loss_value()
      • NetRunAgent.get_parameters_to_update()
      • NetRunAgent.get_stage_dataset_from_config()
      • NetRunAgent.infer()
      • NetRunAgent.run()
      • NetRunAgent.set_datasets()
      • NetRunAgent.set_inferer()
      • NetRunAgent.set_loss_dict()
      • NetRunAgent.set_net_dict()
      • NetRunAgent.set_network()
      • NetRunAgent.set_optimizer()
      • NetRunAgent.set_scheduler()
      • NetRunAgent.set_transform_dict()
      • NetRunAgent.train_valid()
      • NetRunAgent.training()
      • NetRunAgent.validation()
      • NetRunAgent.write_scalars()
    • seed_torch()
  • pymic.net_run.agent_cls module
    • ClassificationAgent
      • ClassificationAgent.create_loss_calculator()
      • ClassificationAgent.create_network()
      • ClassificationAgent.get_evaluation_score()
      • ClassificationAgent.get_loss_value()
      • ClassificationAgent.get_parameters_to_update()
      • ClassificationAgent.get_stage_dataset_from_config()
      • ClassificationAgent.infer()
      • ClassificationAgent.train_valid()
      • ClassificationAgent.training()
      • ClassificationAgent.validation()
      • ClassificationAgent.write_scalars()
    • random()
  • pymic.net_run.agent_seg module
    • SegmentationAgent
      • SegmentationAgent.create_loss_calculator()
      • SegmentationAgent.create_network()
      • SegmentationAgent.get_loss_value()
      • SegmentationAgent.get_parameters_to_update()
      • SegmentationAgent.get_stage_dataset_from_config()
      • SegmentationAgent.infer()
      • SegmentationAgent.infer_with_multiple_checkpoints()
      • SegmentationAgent.save_outputs()
      • SegmentationAgent.set_postprocessor()
      • SegmentationAgent.train_valid()
      • SegmentationAgent.training()
      • SegmentationAgent.validation()
      • SegmentationAgent.write_scalars()
    • random()
  • pymic.net_run.get_optimizer module
    • get_lr_scheduler()
    • get_optimizer()
  • pymic.net_run.infer_func module
    • Inferer
      • Inferer.run()
  • Module contents
• pymic.transform package
  • Submodules
  • pymic.transform.abstract_transform module
    • AbstractTransform
      • AbstractTransform.inverse_transform_for_prediction()
  • pymic.transform.crop module
    • CenterCrop
      • CenterCrop.inverse_transform_for_prediction()
    • CropWithBoundingBox
    • RandomCrop
    • RandomResizedCrop
  • pymic.transform.flip module
    • RandomFlip
      • RandomFlip.inverse_transform_for_prediction()
  • pymic.transform.intensity module
    • GammaCorrection
    • GaussianNoise
    • GrayscaleToRGB
    • InOutPainting
    • InPainting
    • LocalShuffling
    • NonLinearTransform
    • OutPainting
    • bernstein_poly()
    • bezier_curve()
  • pymic.transform.label_convert module
    • LabelConvert
    • LabelConvertNonzero
    • LabelToProbability
    • PartialLabelToProbability
    • ReduceLabelDim
  • pymic.transform.normalize module
    • NormalizeWithMeanStd
    • NormalizeWithMinMax
    • NormalizeWithPercentiles
  • pymic.transform.pad module
    • Pad
      • Pad.inverse_transform_for_prediction()
  • pymic.transform.rescale module
    • RandomRescale
      • RandomRescale.inverse_transform_for_prediction()
    • Rescale
      • Rescale.inverse_transform_for_prediction()
  • pymic.transform.rotate module
    • RandomRotate
      • RandomRotate.inverse_transform_for_prediction()
  • pymic.transform.threshold module
    • ChannelWiseThreshold
    • ChannelWiseThresholdWithNormalize
  • pymic.transform.trans_dict module
  • Module contents
• pymic.util package
  • Submodules
  • pymic.util.evaluation_cls module
    • accuracy()
    • binary_evaluation()
    • get_evaluation_score()
    • main()
    • nexcl_evaluation()
    • sensitivity()
    • specificity()
  • pymic.util.evaluation_seg module
    • binary_assd()
    • binary_dice()
    • binary_hd95()
    • binary_iou()
    • binary_relative_volume_error()
    • dice_of_images()
    • evaluation()
    • get_binary_evaluation_score()
    • get_edge_points()
    • get_multi_class_evaluation_score()
    • main()
  • pymic.util.general module
    • get_one_hot_seg()
    • keyword_match()
    • mixup()
    • tensor_shape_match()
  • pymic.util.image_process module
    • convert_label()
    • crop_ND_volume_with_bounding_box()
    • crop_and_pad_ND_array_to_desired_shape()
    • get_ND_bounding_box()
    • get_euclidean_distance()
    • get_largest_k_components()
    • resample_sitk_image_to_given_spacing()
    • set_ND_volume_roi_with_bounding_box_range()
  • pymic.util.parse_config module
    • is_bool()
    • is_float()
    • is_int()
    • is_list()
    • logging_config()
    • parse_bool()
    • parse_config()
    • parse_list()
    • parse_value_from_string()
    • synchronize_config()
  • pymic.util.post_process module
    • PostKeepLargestComponent
    • PostProcess
  • pymic.util.preprocess module
    • get_transform_list()
    • preprocess_with_transform()
  • pymic.util.ramps module
    • get_rampdown_ratio()
    • get_rampup_ratio()
  • Module contents

Module contents