Index

A

AbstractClassificationLoss (class in pymic.loss.cls.basic) AbstractSegLoss (class in pymic.loss.seg.abstract) AbstractTransform (class in pymic.transform.abstract_transform) accuracy() (in module pymic.util.evaluation_cls)

add_val() (pymic.net_run.noisy_label.nll_dast.Rank method) ASPPBlock (class in pymic.net.net2d.cople_net) AttentionGateBlock (class in pymic.net.net2d.unet2d_attention) AttentionUNet2D (class in pymic.net.net2d.unet2d_attention) AuxiliaryDecoder (class in pymic.net.net2d.unet2d_cct)

B

bernstein_poly() (in module pymic.transform.intensity) bezier_curve() (in module pymic.transform.intensity) binary_assd() (in module pymic.util.evaluation_seg) binary_dice() (in module pymic.util.evaluation_seg) binary_evaluation() (in module pymic.util.evaluation_cls)

binary_hd95() (in module pymic.util.evaluation_seg) binary_iou() (in module pymic.util.evaluation_seg) binary_relative_volume_error() (in module pymic.util.evaluation_seg) BiNet (class in pymic.net_run.noisy_label.nll_co_teaching) (class in pymic.net_run.semi_sup.ssl_cps) BuiltInNet (class in pymic.net.cls.torch_pretrained_net)

C

CenterCrop (class in pymic.transform.crop) ChannelSELayer (class in pymic.net.net2d.scse2d) ChannelSELayer3D (class in pymic.net.net3d.scse3d) ChannelSpatialSELayer (class in pymic.net.net2d.scse2d) ChannelSpatialSELayer3D (class in pymic.net.net3d.scse3d) ChannelToSpace3D (class in pymic.layer.space2channel) ChannelWiseThreshold (class in pymic.transform.threshold) ChannelWiseThresholdWithNormalize (class in pymic.transform.threshold) ClassificationAgent (class in pymic.net_run.agent_cls) ClassificationDataset (class in pymic.io.nifty_dataset) CombinedLoss (class in pymic.loss.seg.combined) ConsistLoss (class in pymic.net_run.noisy_label.nll_dast) ConvBlock (class in pymic.net.net2d.unet2d) (class in pymic.net.net3d.unet3d) ConvBlockND (class in pymic.net.net3d.unet2d5) ConvBNActBlock (class in pymic.net.net2d.cople_net) convert_label() (in module pymic.util.image_process) convert_tensor_type() (pymic.net_run.agent_abstract.NetRunAgent method) ConvLayer (class in pymic.net.net2d.cople_net) ConvolutionLayer (class in pymic.layer.convolution) ConvScSEBlock (class in pymic.net.net2d.unet2d_scse) ConvScSEBlock3D (class in pymic.net.net3d.unet3d_scse) COPLENet (class in pymic.net.net2d.cople_net) create_dataset() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.noisy_label.nll_dast.NLLDAST method) (pymic.net_run.semi_sup.ssl_abstract.SSLSegAgent method)

create_loss_calculator() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) (pymic.net_run.self_sup.self_sl_agent.SelfSLSegAgent method) create_network() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) (pymic.net_run.noisy_label.nll_co_teaching.NLLCoTeaching method) (pymic.net_run.noisy_label.nll_trinet.NLLTriNet method) (pymic.net_run.semi_sup.ssl_cps.SSLCPS method) (pymic.net_run.semi_sup.ssl_mt.SSLMeanTeacher method) (pymic.net_run.weak_sup.wsl_ustm.WSLUSTM method) create_optimizer() (pymic.net_run.agent_abstract.NetRunAgent method) crop_and_pad_ND_array_to_desired_shape() (in module pymic.util.image_process) crop_ND_volume_with_bounding_box() (in module pymic.util.image_process) CropWithBoundingBox (class in pymic.transform.crop) CrossEntropyLoss (class in pymic.loss.cls.basic) (class in pymic.loss.seg.ce) CSE (pymic.net.net2d.scse2d.SELayer attribute) (pymic.net.net3d.scse3d.SELayer attribute) CSSE (pymic.net.net2d.scse2d.SELayer attribute) (pymic.net.net3d.scse3d.SELayer attribute)

D

Decoder (class in pymic.net.net2d.unet2d) (class in pymic.net.net3d.unet3d) DeconvolutionLayer (class in pymic.layer.deconvolution) DeepSuperviseLoss (class in pymic.loss.seg.deep_sup) DepthSeperableConvolutionLayer (class in pymic.layer.convolution) DepthSeperableDeconvolutionLayer (class in pymic.layer.deconvolution) dice_of_images() (in module pymic.util.evaluation_seg)

DiceLoss (class in pymic.loss.seg.dice) DownBlock (class in pymic.net.net2d.cople_net) (class in pymic.net.net2d.unet2d) (class in pymic.net.net2d.unet2d_scse) (class in pymic.net.net3d.unet2d5) (class in pymic.net.net3d.unet3d) (class in pymic.net.net3d.unet3d_scse)

E

Encoder (class in pymic.net.net2d.unet2d) (class in pymic.net.net3d.unet3d)

EntropyLoss (class in pymic.loss.seg.ssl) evaluation() (in module pymic.util.evaluation_seg) ExpLogLoss (class in pymic.loss.seg.exp_log)

F

feature_based_noise() (pymic.net.net2d.unet2d_cct.AuxiliaryDecoder method) feature_drop() (pymic.net.net2d.unet2d_cct.AuxiliaryDecoder method) FocalDiceLoss (class in pymic.loss.seg.dice) forward() (pymic.layer.convolution.ConvolutionLayer method) (pymic.layer.convolution.DepthSeperableConvolutionLayer method) (pymic.layer.deconvolution.DeconvolutionLayer method) (pymic.layer.deconvolution.DepthSeperableDeconvolutionLayer method) (pymic.layer.space2channel.ChannelToSpace3D method) (pymic.layer.space2channel.SpaceToChannel3D method) (pymic.loss.cls.basic.AbstractClassificationLoss method) (pymic.loss.cls.basic.CrossEntropyLoss method) (pymic.loss.cls.basic.L1Loss method) (pymic.loss.cls.basic.MSELoss method) (pymic.loss.cls.basic.NLLLoss method) (pymic.loss.cls.basic.SigmoidCELoss method) (pymic.loss.seg.abstract.AbstractSegLoss method) (pymic.loss.seg.ce.CrossEntropyLoss method) (pymic.loss.seg.ce.GeneralizedCELoss method) (pymic.loss.seg.combined.CombinedLoss method) (pymic.loss.seg.deep_sup.DeepSuperviseLoss method) (pymic.loss.seg.dice.DiceLoss method) (pymic.loss.seg.dice.FocalDiceLoss method) (pymic.loss.seg.dice.NoiseRobustDiceLoss method) (pymic.loss.seg.exp_log.ExpLogLoss method) (pymic.loss.seg.gatedcrf.GatedCRFLoss method) (pymic.loss.seg.mse.MAELoss method) (pymic.loss.seg.mse.MSELoss method) (pymic.loss.seg.mumford_shah.MumfordShahLoss method) (pymic.loss.seg.slsr.SLSRLoss method) (pymic.loss.seg.ssl.EntropyLoss method) (pymic.loss.seg.ssl.TotalVariationLoss method) (pymic.net.cls.torch_pretrained_net.BuiltInNet method) (pymic.net.net2d.cople_net.ASPPBlock method) (pymic.net.net2d.cople_net.ConvBNActBlock method) (pymic.net.net2d.cople_net.ConvLayer method) (pymic.net.net2d.cople_net.COPLENet method) (pymic.net.net2d.cople_net.DownBlock method) (pymic.net.net2d.cople_net.SEBlock method) (pymic.net.net2d.cople_net.UpBlock method) (pymic.net.net2d.scse2d.ChannelSELayer method) (pymic.net.net2d.scse2d.ChannelSpatialSELayer method) (pymic.net.net2d.scse2d.SpatialSELayer method) (pymic.net.net2d.unet2d.ConvBlock method) (pymic.net.net2d.unet2d.Decoder method) (pymic.net.net2d.unet2d.DownBlock method) (pymic.net.net2d.unet2d.Encoder method) (pymic.net.net2d.unet2d.UNet2D method) (pymic.net.net2d.unet2d.UpBlock method) (pymic.net.net2d.unet2d_attention.AttentionGateBlock method) (pymic.net.net2d.unet2d_attention.UpBlockWithAttention method) (pymic.net.net2d.unet2d_cct.AuxiliaryDecoder method) (pymic.net.net2d.unet2d_cct.UNet2D_CCT method) (pymic.net.net2d.unet2d_dual_branch.UNet2D_DualBranch method) (pymic.net.net2d.unet2d_nest.NestedUNet2D method) (pymic.net.net2d.unet2d_scse.ConvScSEBlock method) (pymic.net.net2d.unet2d_scse.DownBlock method) (pymic.net.net2d.unet2d_scse.UNet2D_ScSE method) (pymic.net.net2d.unet2d_scse.UpBlock method) (pymic.net.net3d.scse3d.ChannelSELayer3D method) (pymic.net.net3d.scse3d.ChannelSpatialSELayer3D method) (pymic.net.net3d.scse3d.SpatialSELayer3D method) (pymic.net.net3d.unet2d5.ConvBlockND method) (pymic.net.net3d.unet2d5.DownBlock method) (pymic.net.net3d.unet2d5.UNet2D5 method) (pymic.net.net3d.unet2d5.UpBlock method) (pymic.net.net3d.unet3d.ConvBlock method) (pymic.net.net3d.unet3d.Decoder method) (pymic.net.net3d.unet3d.DownBlock method) (pymic.net.net3d.unet3d.Encoder method) (pymic.net.net3d.unet3d.UNet3D method) (pymic.net.net3d.unet3d.UpBlock method) (pymic.net.net3d.unet3d_scse.ConvScSEBlock3D method) (pymic.net.net3d.unet3d_scse.DownBlock method) (pymic.net.net3d.unet3d_scse.UNet3D_ScSE method) (pymic.net.net3d.unet3d_scse.UpBlock method) (pymic.net_run.noisy_label.nll_co_teaching.BiNet method) (pymic.net_run.noisy_label.nll_dast.ConsistLoss method) (pymic.net_run.noisy_label.nll_trinet.TriNet method) (pymic.net_run.semi_sup.ssl_cps.BiNet method)

G

GammaCorrection (class in pymic.transform.intensity) GatedCRFLoss (class in pymic.loss.seg.gatedcrf) GaussianNoise (class in pymic.transform.intensity) GeneralizedCELoss (class in pymic.loss.seg.ce) get_acti_func() (in module pymic.layer.activation) get_binary_evaluation_score() (in module pymic.util.evaluation_seg) get_ce() (in module pymic.net_run.noisy_label.nll_dast) get_checkpoint_name() (pymic.net_run.agent_abstract.NetRunAgent method) get_classwise_dice() (in module pymic.loss.seg.util) get_confidence_map() (in module pymic.net_run.noisy_label.nll_clslsr) get_confident_map() (in module pymic.net_run.noisy_label.nll_clslsr) get_edge_points() (in module pymic.util.evaluation_seg) get_euclidean_distance() (in module pymic.util.image_process) get_evaluation_score() (in module pymic.util.evaluation_cls) (pymic.net_run.agent_cls.ClassificationAgent method) get_gradient_loss() (pymic.loss.seg.mumford_shah.MumfordShahLoss method) get_largest_k_components() (in module pymic.util.image_process) get_levelset_loss() (pymic.loss.seg.mumford_shah.MumfordShahLoss method) get_loss_and_confident_mask() (pymic.net_run.noisy_label.nll_trinet.NLLTriNet method) get_loss_value() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) get_lr_scheduler() (in module pymic.net_run.get_optimizer)

get_multi_class_evaluation_score() (in module pymic.util.evaluation_seg) get_ND_bounding_box() (in module pymic.util.image_process) get_noisy_dataset_from_config() (pymic.net_run.noisy_label.nll_dast.NLLDAST method) get_one_hot_seg() (in module pymic.util.general) get_optimizer() (in module pymic.net_run.get_optimizer) get_parameters_to_update() (pymic.net.cls.torch_pretrained_net.BuiltInNet method) (pymic.net.cls.torch_pretrained_net.MobileNetV2 method) (pymic.net.cls.torch_pretrained_net.ResNet18 method) (pymic.net.cls.torch_pretrained_net.VGG16 method) (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) get_rampdown_ratio() (in module pymic.util.ramps) get_rampup_ratio() (in module pymic.util.ramps) get_soft_label() (in module pymic.loss.cls.util) (in module pymic.loss.seg.util) get_stage_dataset_from_config() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) get_transform_list() (in module pymic.util.preprocess) get_unlabeled_dataset_from_config() (pymic.net_run.semi_sup.ssl_abstract.SSLSegAgent method) GrayscaleToRGB (class in pymic.transform.intensity) grouper() (in module pymic.io.h5_dataset)

H

H5DataSet (class in pymic.io.h5_dataset)

I

infer() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) infer_with_cl() (pymic.net_run.noisy_label.nll_clslsr.NLLCLSLSR method) infer_with_multiple_checkpoints() (pymic.net_run.agent_seg.SegmentationAgent method) Inferer (class in pymic.net_run.infer_func) InOutPainting (class in pymic.transform.intensity) InPainting (class in pymic.transform.intensity) inverse_transform_for_prediction() (pymic.transform.abstract_transform.AbstractTransform method) (pymic.transform.crop.CenterCrop method) (pymic.transform.flip.RandomFlip method) (pymic.transform.pad.Pad method) (pymic.transform.rescale.RandomRescale method) (pymic.transform.rescale.Rescale method) (pymic.transform.rotate.RandomRotate method)

is_bool() (in module pymic.util.parse_config) is_float() (in module pymic.util.parse_config) is_int() (in module pymic.util.parse_config) is_list() (in module pymic.util.parse_config) iterate_eternally() (in module pymic.io.h5_dataset) iterate_once() (in module pymic.io.h5_dataset)

K

keyword_match() (in module pymic.util.general)

kl_div_map() (pymic.net_run.noisy_label.nll_dast.ConsistLoss method) kl_loss() (pymic.net_run.noisy_label.nll_dast.ConsistLoss method)

L

L1Loss (class in pymic.loss.cls.basic) LabelConvert (class in pymic.transform.label_convert) LabelConvertNonzero (class in pymic.transform.label_convert) LabelToProbability (class in pymic.transform.label_convert)

load_image_as_nd_array() (in module pymic.io.image_read_write) load_nifty_volume_as_4d_array() (in module pymic.io.image_read_write) load_rgb_image_as_3d_array() (in module pymic.io.image_read_write) LocalShuffling (class in pymic.transform.intensity) logging_config() (in module pymic.util.parse_config)

M

MAELoss (class in pymic.loss.seg.mse) main() (in module pymic.util.evaluation_cls) (in module pymic.util.evaluation_seg) match_prediction_and_gt_shape() (in module pymic.loss.seg.deep_sup) mixup() (in module pymic.util.general) MobileNetV2 (class in pymic.net.cls.torch_pretrained_net) module pymic pymic.io pymic.io.h5_dataset pymic.io.image_read_write pymic.io.nifty_dataset pymic.layer pymic.layer.activation pymic.layer.convolution pymic.layer.deconvolution pymic.layer.space2channel pymic.loss pymic.loss.cls pymic.loss.cls.basic pymic.loss.cls.util pymic.loss.loss_dict_cls pymic.loss.loss_dict_seg pymic.loss.seg pymic.loss.seg.abstract pymic.loss.seg.ce pymic.loss.seg.combined pymic.loss.seg.deep_sup pymic.loss.seg.dice pymic.loss.seg.exp_log pymic.loss.seg.gatedcrf pymic.loss.seg.mse pymic.loss.seg.mumford_shah pymic.loss.seg.slsr pymic.loss.seg.ssl pymic.loss.seg.util pymic.net pymic.net.cls pymic.net.cls.torch_pretrained_net pymic.net.net2d pymic.net.net2d.cople_net pymic.net.net2d.scse2d pymic.net.net2d.unet2d pymic.net.net2d.unet2d_attention pymic.net.net2d.unet2d_cct pymic.net.net2d.unet2d_dual_branch pymic.net.net2d.unet2d_nest pymic.net.net2d.unet2d_scse pymic.net.net3d pymic.net.net3d.scse3d pymic.net.net3d.unet2d5 pymic.net.net3d.unet3d pymic.net.net3d.unet3d_scse pymic.net.net_dict_cls pymic.net.net_dict_seg pymic.net_run pymic.net_run.agent_abstract pymic.net_run.agent_cls pymic.net_run.agent_seg pymic.net_run.get_optimizer pymic.net_run.infer_func pymic.net_run.noisy_label pymic.net_run.noisy_label.nll_clslsr pymic.net_run.noisy_label.nll_co_teaching pymic.net_run.noisy_label.nll_dast pymic.net_run.noisy_label.nll_trinet pymic.net_run.self_sup pymic.net_run.self_sup.self_sl_agent pymic.net_run.semi_sup pymic.net_run.semi_sup.ssl_abstract pymic.net_run.semi_sup.ssl_cct pymic.net_run.semi_sup.ssl_cps pymic.net_run.semi_sup.ssl_em pymic.net_run.semi_sup.ssl_mt pymic.net_run.semi_sup.ssl_uamt pymic.net_run.semi_sup.ssl_urpc pymic.net_run.weak_sup pymic.net_run.weak_sup.wsl_abstract pymic.net_run.weak_sup.wsl_dmpls pymic.net_run.weak_sup.wsl_em pymic.net_run.weak_sup.wsl_gatedcrf pymic.net_run.weak_sup.wsl_mumford_shah pymic.net_run.weak_sup.wsl_tv pymic.net_run.weak_sup.wsl_ustm pymic.transform pymic.transform.abstract_transform pymic.transform.crop pymic.transform.flip pymic.transform.intensity pymic.transform.label_convert pymic.transform.normalize pymic.transform.pad pymic.transform.rescale pymic.transform.rotate pymic.transform.threshold pymic.transform.trans_dict pymic.util pymic.util.evaluation_cls pymic.util.evaluation_seg pymic.util.general pymic.util.image_process pymic.util.parse_config pymic.util.post_process pymic.util.preprocess pymic.util.ramps

MSELoss (class in pymic.loss.cls.basic) (class in pymic.loss.seg.mse) MumfordShahLoss (class in pymic.loss.seg.mumford_shah)

N

NestedUNet2D (class in pymic.net.net2d.unet2d_nest) NetRunAgent (class in pymic.net_run.agent_abstract) nexcl_evaluation() (in module pymic.util.evaluation_cls) NiftyDataset (class in pymic.io.nifty_dataset) NLLCLSLSR (class in pymic.net_run.noisy_label.nll_clslsr) NLLCoTeaching (class in pymic.net_run.noisy_label.nll_co_teaching) NLLDAST (class in pymic.net_run.noisy_label.nll_dast) NLLLoss (class in pymic.loss.cls.basic)

NLLTriNet (class in pymic.net_run.noisy_label.nll_trinet) NoiseRobustDiceLoss (class in pymic.loss.seg.dice) NONE (pymic.net.net2d.scse2d.SELayer attribute) (pymic.net.net3d.scse3d.SELayer attribute) NonLinearTransform (class in pymic.transform.intensity) NormalizeWithMeanStd (class in pymic.transform.normalize) NormalizeWithMinMax (class in pymic.transform.normalize) NormalizeWithPercentiles (class in pymic.transform.normalize)

O

OutPainting (class in pymic.transform.intensity)

P

Pad (class in pymic.transform.pad) parse_bool() (in module pymic.util.parse_config) parse_config() (in module pymic.util.parse_config) parse_list() (in module pymic.util.parse_config) parse_value_from_string() (in module pymic.util.parse_config) PartialLabelToProbability (class in pymic.transform.label_convert) PostKeepLargestComponent (class in pymic.util.post_process) PostProcess (class in pymic.util.post_process) preprocess_with_transform() (in module pymic.util.preprocess) pymic module pymic.io module pymic.io.h5_dataset module pymic.io.image_read_write module pymic.io.nifty_dataset module pymic.layer module pymic.layer.activation module pymic.layer.convolution module pymic.layer.deconvolution module pymic.layer.space2channel module pymic.loss module pymic.loss.cls module pymic.loss.cls.basic module pymic.loss.cls.util module pymic.loss.loss_dict_cls module pymic.loss.loss_dict_seg module pymic.loss.seg module 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 pymic.net module pymic.net.cls module pymic.net.cls.torch_pretrained_net module pymic.net.net2d module 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.net3d module pymic.net.net3d.scse3d module pymic.net.net3d.unet2d5 module pymic.net.net3d.unet3d module pymic.net.net3d.unet3d_scse module pymic.net.net_dict_cls module

pymic.net.net_dict_seg module pymic.net_run module pymic.net_run.agent_abstract module pymic.net_run.agent_cls module pymic.net_run.agent_seg module pymic.net_run.get_optimizer module pymic.net_run.infer_func module pymic.net_run.noisy_label module 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 pymic.net_run.self_sup module pymic.net_run.self_sup.self_sl_agent module pymic.net_run.semi_sup module 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 pymic.net_run.weak_sup module 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 pymic.transform module pymic.transform.abstract_transform module pymic.transform.crop module pymic.transform.flip module pymic.transform.intensity module pymic.transform.label_convert module pymic.transform.normalize module pymic.transform.pad module pymic.transform.rescale module pymic.transform.rotate module pymic.transform.threshold module pymic.transform.trans_dict module pymic.util module pymic.util.evaluation_cls module pymic.util.evaluation_seg module pymic.util.general module pymic.util.image_process module pymic.util.parse_config module pymic.util.post_process module pymic.util.preprocess module pymic.util.ramps module

R

random() (in module pymic.net_run.agent_cls) (in module pymic.net_run.agent_seg) (in module pymic.net_run.self_sup.self_sl_agent) RandomCrop (class in pymic.transform.crop) RandomFlip (class in pymic.transform.flip) RandomRescale (class in pymic.transform.rescale) RandomResizedCrop (class in pymic.transform.crop) RandomRotate (class in pymic.transform.rotate) Rank (class in pymic.net_run.noisy_label.nll_dast)

ReduceLabelDim (class in pymic.transform.label_convert) resample_sitk_image_to_given_spacing() (in module pymic.util.image_process) Rescale (class in pymic.transform.rescale) reshape_prediction_and_ground_truth() (in module pymic.loss.seg.util) reshape_tensor_to_2D() (in module pymic.loss.seg.util) ResNet18 (class in pymic.net.cls.torch_pretrained_net) rotate_nifty_volume_to_LPS() (in module pymic.io.image_read_write) run() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.infer_func.Inferer method)

S

save_array_as_nifty_volume() (in module pymic.io.image_read_write) save_array_as_rgb_image() (in module pymic.io.image_read_write) save_nd_array_as_image() (in module pymic.io.image_read_write) save_outputs() (pymic.net_run.agent_seg.SegmentationAgent method) SEBlock (class in pymic.net.net2d.cople_net) seed_torch() (in module pymic.net_run.agent_abstract) SegmentationAgent (class in pymic.net_run.agent_seg) SELayer (class in pymic.net.net2d.scse2d) (class in pymic.net.net3d.scse3d) select_criterion() (in module pymic.net_run.noisy_label.nll_dast) SelfSLSegAgent (class in pymic.net_run.self_sup.self_sl_agent) sensitivity() (in module pymic.util.evaluation_cls) set_datasets() (pymic.net_run.agent_abstract.NetRunAgent method) set_inferer() (pymic.net_run.agent_abstract.NetRunAgent method) set_loss_dict() (pymic.net_run.agent_abstract.NetRunAgent method) set_ND_volume_roi_with_bounding_box_range() (in module pymic.util.image_process) set_net_dict() (pymic.net_run.agent_abstract.NetRunAgent method) set_network() (pymic.net_run.agent_abstract.NetRunAgent method) set_optimizer() (pymic.net_run.agent_abstract.NetRunAgent method) set_postprocessor() (pymic.net_run.agent_seg.SegmentationAgent method)

set_scheduler() (pymic.net_run.agent_abstract.NetRunAgent method) set_transform_dict() (pymic.net_run.agent_abstract.NetRunAgent method) SigmoidCELoss (class in pymic.loss.cls.basic) SLSRLoss (class in pymic.loss.seg.slsr) softmax_js_loss() (in module pymic.net_run.semi_sup.ssl_cct) softmax_kl_loss() (in module pymic.net_run.semi_sup.ssl_cct) softmax_mse_loss() (in module pymic.net_run.semi_sup.ssl_cct) SpaceToChannel3D (class in pymic.layer.space2channel) SpatialSELayer (class in pymic.net.net2d.scse2d) SpatialSELayer3D (class in pymic.net.net3d.scse3d) specificity() (in module pymic.util.evaluation_cls) SSE (pymic.net.net2d.scse2d.SELayer attribute) (pymic.net.net3d.scse3d.SELayer attribute) SSLCCT (class in pymic.net_run.semi_sup.ssl_cct) SSLCPS (class in pymic.net_run.semi_sup.ssl_cps) SSLEntropyMinimization (class in pymic.net_run.semi_sup.ssl_em) SSLMeanTeacher (class in pymic.net_run.semi_sup.ssl_mt) SSLSegAgent (class in pymic.net_run.semi_sup.ssl_abstract) SSLUncertaintyAwareMeanTeacher (class in pymic.net_run.semi_sup.ssl_uamt) SSLURPC (class in pymic.net_run.semi_sup.ssl_urpc) synchronize_config() (in module pymic.util.parse_config)

T

tensor_shape_match() (in module pymic.util.general) TotalVariationLoss (class in pymic.loss.seg.ssl) train_valid() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) (pymic.net_run.noisy_label.nll_dast.NLLDAST method) (pymic.net_run.self_sup.self_sl_agent.SelfSLSegAgent method) (pymic.net_run.semi_sup.ssl_abstract.SSLSegAgent method) training (pymic.layer.convolution.ConvolutionLayer attribute) (pymic.layer.convolution.DepthSeperableConvolutionLayer attribute) (pymic.layer.deconvolution.DeconvolutionLayer attribute) (pymic.layer.deconvolution.DepthSeperableDeconvolutionLayer attribute) (pymic.layer.space2channel.ChannelToSpace3D attribute) (pymic.layer.space2channel.SpaceToChannel3D attribute) (pymic.loss.cls.basic.AbstractClassificationLoss attribute) (pymic.loss.cls.basic.CrossEntropyLoss attribute) (pymic.loss.cls.basic.L1Loss attribute) (pymic.loss.cls.basic.MSELoss attribute) (pymic.loss.cls.basic.NLLLoss attribute) (pymic.loss.cls.basic.SigmoidCELoss attribute) (pymic.loss.seg.abstract.AbstractSegLoss attribute) (pymic.loss.seg.ce.CrossEntropyLoss attribute) (pymic.loss.seg.ce.GeneralizedCELoss attribute) (pymic.loss.seg.combined.CombinedLoss attribute) (pymic.loss.seg.deep_sup.DeepSuperviseLoss attribute) (pymic.loss.seg.dice.DiceLoss attribute) (pymic.loss.seg.dice.FocalDiceLoss attribute) (pymic.loss.seg.dice.NoiseRobustDiceLoss attribute) (pymic.loss.seg.exp_log.ExpLogLoss attribute) (pymic.loss.seg.gatedcrf.GatedCRFLoss attribute) (pymic.loss.seg.mse.MAELoss attribute) (pymic.loss.seg.mse.MSELoss attribute) (pymic.loss.seg.mumford_shah.MumfordShahLoss attribute) (pymic.loss.seg.slsr.SLSRLoss attribute) (pymic.loss.seg.ssl.EntropyLoss attribute) (pymic.loss.seg.ssl.TotalVariationLoss attribute) (pymic.net.cls.torch_pretrained_net.BuiltInNet attribute) (pymic.net.cls.torch_pretrained_net.MobileNetV2 attribute) (pymic.net.cls.torch_pretrained_net.ResNet18 attribute) (pymic.net.cls.torch_pretrained_net.VGG16 attribute) (pymic.net.net2d.cople_net.ASPPBlock attribute) (pymic.net.net2d.cople_net.ConvBNActBlock attribute) (pymic.net.net2d.cople_net.ConvLayer attribute) (pymic.net.net2d.cople_net.COPLENet attribute) (pymic.net.net2d.cople_net.DownBlock attribute) (pymic.net.net2d.cople_net.SEBlock attribute) (pymic.net.net2d.cople_net.UpBlock attribute) (pymic.net.net2d.scse2d.ChannelSELayer attribute) (pymic.net.net2d.scse2d.ChannelSpatialSELayer attribute) (pymic.net.net2d.scse2d.SpatialSELayer attribute) (pymic.net.net2d.unet2d.ConvBlock attribute) (pymic.net.net2d.unet2d.Decoder attribute) (pymic.net.net2d.unet2d.DownBlock attribute) (pymic.net.net2d.unet2d.Encoder attribute) (pymic.net.net2d.unet2d.UNet2D attribute) (pymic.net.net2d.unet2d.UpBlock attribute) (pymic.net.net2d.unet2d_attention.AttentionGateBlock attribute) (pymic.net.net2d.unet2d_attention.AttentionUNet2D attribute) (pymic.net.net2d.unet2d_attention.UpBlockWithAttention attribute) (pymic.net.net2d.unet2d_cct.AuxiliaryDecoder attribute) (pymic.net.net2d.unet2d_cct.UNet2D_CCT attribute) (pymic.net.net2d.unet2d_dual_branch.UNet2D_DualBranch attribute) (pymic.net.net2d.unet2d_nest.NestedUNet2D attribute) (pymic.net.net2d.unet2d_scse.ConvScSEBlock attribute) (pymic.net.net2d.unet2d_scse.DownBlock attribute) (pymic.net.net2d.unet2d_scse.UNet2D_ScSE attribute) (pymic.net.net2d.unet2d_scse.UpBlock attribute) (pymic.net.net3d.scse3d.ChannelSELayer3D attribute) (pymic.net.net3d.scse3d.ChannelSpatialSELayer3D attribute) (pymic.net.net3d.scse3d.SpatialSELayer3D attribute) (pymic.net.net3d.unet2d5.ConvBlockND attribute) (pymic.net.net3d.unet2d5.DownBlock attribute) (pymic.net.net3d.unet2d5.UNet2D5 attribute) (pymic.net.net3d.unet2d5.UpBlock attribute) (pymic.net.net3d.unet3d.ConvBlock attribute) (pymic.net.net3d.unet3d.Decoder attribute) (pymic.net.net3d.unet3d.DownBlock attribute) (pymic.net.net3d.unet3d.Encoder attribute) (pymic.net.net3d.unet3d.UNet3D attribute) (pymic.net.net3d.unet3d.UpBlock attribute) (pymic.net.net3d.unet3d_scse.ConvScSEBlock3D attribute) (pymic.net.net3d.unet3d_scse.DownBlock attribute) (pymic.net.net3d.unet3d_scse.UNet3D_ScSE attribute) (pymic.net.net3d.unet3d_scse.UpBlock attribute) (pymic.net_run.noisy_label.nll_co_teaching.BiNet attribute) (pymic.net_run.noisy_label.nll_dast.ConsistLoss attribute) (pymic.net_run.noisy_label.nll_trinet.TriNet attribute) (pymic.net_run.semi_sup.ssl_cps.BiNet attribute)

training() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) (pymic.net_run.noisy_label.nll_co_teaching.NLLCoTeaching method) (pymic.net_run.noisy_label.nll_dast.NLLDAST method) (pymic.net_run.noisy_label.nll_trinet.NLLTriNet method) (pymic.net_run.self_sup.self_sl_agent.SelfSLSegAgent method) (pymic.net_run.semi_sup.ssl_cct.SSLCCT method) (pymic.net_run.semi_sup.ssl_cps.SSLCPS method) (pymic.net_run.semi_sup.ssl_em.SSLEntropyMinimization method) (pymic.net_run.semi_sup.ssl_mt.SSLMeanTeacher method) (pymic.net_run.semi_sup.ssl_uamt.SSLUncertaintyAwareMeanTeacher method) (pymic.net_run.semi_sup.ssl_urpc.SSLURPC method) (pymic.net_run.weak_sup.wsl_dmpls.WSLDMPLS method) (pymic.net_run.weak_sup.wsl_em.WSLEntropyMinimization method) (pymic.net_run.weak_sup.wsl_gatedcrf.WSLGatedCRF method) (pymic.net_run.weak_sup.wsl_mumford_shah.WSLMumfordShah method) (pymic.net_run.weak_sup.wsl_tv.WSLTotalVariation method) (pymic.net_run.weak_sup.wsl_ustm.WSLUSTM method) TriNet (class in pymic.net_run.noisy_label.nll_trinet) TwoStreamBatchSampler (class in pymic.io.h5_dataset)

U

UNet2D (class in pymic.net.net2d.unet2d) UNet2D5 (class in pymic.net.net3d.unet2d5) UNet2D_CCT (class in pymic.net.net2d.unet2d_cct) UNet2D_DualBranch (class in pymic.net.net2d.unet2d_dual_branch) UNet2D_ScSE (class in pymic.net.net2d.unet2d_scse) UNet3D (class in pymic.net.net3d.unet3d) UNet3D_ScSE (class in pymic.net.net3d.unet3d_scse)

UpBlock (class in pymic.net.net2d.cople_net) (class in pymic.net.net2d.unet2d) (class in pymic.net.net2d.unet2d_scse) (class in pymic.net.net3d.unet2d5) (class in pymic.net.net3d.unet3d) (class in pymic.net.net3d.unet3d_scse) UpBlockWithAttention (class in pymic.net.net2d.unet2d_attention)

V

validation() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) (pymic.net_run.self_sup.self_sl_agent.SelfSLSegAgent method)

VGG16 (class in pymic.net.cls.torch_pretrained_net)

W

write_scalars() (pymic.net_run.agent_abstract.NetRunAgent method) (pymic.net_run.agent_cls.ClassificationAgent method) (pymic.net_run.agent_seg.SegmentationAgent method) (pymic.net_run.noisy_label.nll_co_teaching.NLLCoTeaching method) (pymic.net_run.noisy_label.nll_trinet.NLLTriNet method) (pymic.net_run.self_sup.self_sl_agent.SelfSLSegAgent method) (pymic.net_run.semi_sup.ssl_abstract.SSLSegAgent method) (pymic.net_run.semi_sup.ssl_cps.SSLCPS method) (pymic.net_run.weak_sup.wsl_abstract.WSLSegAgent method)

WSLDMPLS (class in pymic.net_run.weak_sup.wsl_dmpls) WSLEntropyMinimization (class in pymic.net_run.weak_sup.wsl_em) WSLGatedCRF (class in pymic.net_run.weak_sup.wsl_gatedcrf) WSLMumfordShah (class in pymic.net_run.weak_sup.wsl_mumford_shah) WSLSegAgent (class in pymic.net_run.weak_sup.wsl_abstract) WSLTotalVariation (class in pymic.net_run.weak_sup.wsl_tv) WSLUSTM (class in pymic.net_run.weak_sup.wsl_ustm)