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NiftyNet 0.6.0 documentation
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__init__ (ImageSetsPartitioner attribute)
(NiftyNetGlobalConfig attribute)
__init__() (AdditiveUpsampleLayer method)
(AffineAugmentationLayer method)
(AffineGridWarperLayer method)
(AffineWarpConstraints method)
(BSplineFieldImageGridWarperLayer method)
(BottleneckBlock method)
,
[1]
(CRFAsRNNLayer method)
(ConvDecoder method)
(ConvEncoder method)
(ConvLayer method)
(ConvolutionalLayer method)
(DataFrameAggregator method)
(DeepMedic method)
(DenseFeatureStackBlock method)
(DenseFeatureStackBlockWithSkipAndDownsample method)
(DenseVNet method)
(DownResBlock method)
,
[1]
(FCDecoder method)
(GaussianSampler method)
(GridWarperLayer method)
(HighRes3DNet method)
(HighRes3DNetLarge method)
(HighRes3DNetSmall method)
(HighResBlock method)
(HistogramNormalisationLayer method)
(HolisticNet method)
(INetAffine method)
(INetDense method)
(INetHybridPreWarp method)
(INetHybridTwoStream method)
(ImageDiscriminator method)
,
[1]
(ImageGenerator method)
,
[1]
(ImageWindow method)
(LinearResizeLayer method)
(MergeLayer method)
(PadLayer method)
(RandomElasticDeformationLayer method)
(RandomFlipLayer method)
(ResNet method)
(ResampledFieldGridWarperLayer method)
(RescaledFieldImageGridWarperLayer method)
(ResidualUnit method)
(SE_ResNet method)
(ScalarAggregator method)
(ScaleBlock method)
(ScaleNet method)
(ScoreLayer method)
(SmoothingLayer method)
(SpatialPriorBlock method)
(SubPixelLayer method)
(ToyNet method)
(UNet3D method)
(UNetBlock method)
(VAE method)
(VNet method)
(VNetBlock method)
A
accuracy (class in niftynet.evaluation.classification_evaluations)
(class in niftynet.evaluation.segmentation_evaluations)
accuracy() (PairwiseMeasures method)
ActiLayer (class in niftynet.layer.activation)
action (BaseApplication attribute)
Adagrad (class in niftynet.engine.application_optimiser)
Adam (class in niftynet.engine.application_optimiser)
add_application_args() (in module niftynet.utilities.user_parameters_default)
add_confusion_matrix_summaries_() (ClassificationApplication method)
,
[1]
(MultiClassifSegApplication method)
add_customised_args() (in module niftynet.utilities.user_parameters_custom)
add_evaluation_args() (in module niftynet.utilities.user_parameters_default)
add_gradients() (ApplyGradients method)
add_inference_args() (in module niftynet.utilities.user_parameters_default)
add_inferred_output() (ClassificationApplication method)
,
[1]
(MultiClassifSegApplication method)
(RegressionApplication method)
,
[1]
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
add_inferred_output_like() (BaseApplication method)
add_input_data_args() (in module niftynet.utilities.user_parameters_default)
add_input_name_args() (in module niftynet.utilities.user_parameters_helper)
add_network_args() (in module niftynet.utilities.user_parameters_default)
add_preprocessing_layers() (ImageReader method)
add_to_collection() (GradientsCollector method)
(OutputsCollector method)
add_training_args() (in module niftynet.utilities.user_parameters_default)
add_validation_flag() (BaseApplication method)
AdditiveUpsampleLayer (class in niftynet.layer.additive_upsample)
AffineAugmentationLayer (class in niftynet.layer.affine_augmentation)
AffineGridWarperLayer (class in niftynet.layer.grid_warper)
AffineWarpConstraints (class in niftynet.layer.grid_warper)
aggregate() (accuracy method)
(BaseEvaluator method)
(niftynet.contrib.evaluation.classification_evaluations.roc class method)
(niftynet.contrib.evaluation.classification_evaluations.roc_auc class method)
all_files (ImageSetsPartitioner attribute)
angular_second_moment() (RegionProperties method)
ApplicationDriver (class in niftynet.engine.application_driver)
ApplicationFactory (class in niftynet.engine.application_factory)
ApplicationNetFactory (class in niftynet.engine.application_factory)
apply_niftynet_format_to_data() (CSVReader static method)
ApplyGradients (class in niftynet.engine.handler_gradient)
AutoencoderApplication (class in niftynet.application.autoencoder_application)
(class in niftynet.contrib.csv_reader.applications_maybe.autoencoder_application)
available_keywords() (in module niftynet.utilities.user_parameters_parser)
average_distance (class in niftynet.evaluation.segmentation_evaluations)
average_gradients() (in module niftynet.utilities.util_common)
average_multi_opt_gradients() (in module niftynet.utilities.util_common)
B
balanced_spatial_coordinates() (in module niftynet.contrib.csv_reader.sampler_balanced_v2_csv)
(in module niftynet.engine.sampler_balanced_v2)
BalancedSampler (class in niftynet.engine.sampler_balanced_v2)
BalancedSamplerCSV (class in niftynet.contrib.csv_reader.sampler_balanced_v2_csv)
BaseApplication (class in niftynet.application.base_application)
BaseDiscriminator (class in niftynet.layer.gan_blocks)
BaseEvaluation (class in niftynet.evaluation.base_evaluations)
BaseEvaluator (class in niftynet.evaluation.base_evaluator)
BaseGenerator (class in niftynet.layer.gan_blocks)
BaseNet (class in niftynet.network.base_net)
BaseRegressionEvaluation (class in niftynet.evaluation.regression_evaluations)
BinaryMaskingLayer (class in niftynet.layer.binary_masking)
blocks (DownResBlockDesc attribute)
,
[1]
(ResNetDesc attribute)
(SE_ResNetDesc attribute)
bn (ResNetDesc attribute)
(SE_ResNetDesc attribute)
BNLayer (class in niftynet.layer.bn)
border_distance (PairwiseMeasures attribute)
border_map() (MorphologyOps method)
BottleneckBlock (class in niftynet.network.resnet)
(class in niftynet.network.se_resnet)
BottleneckBlockDesc1 (class in niftynet.network.resnet)
(class in niftynet.network.se_resnet)
BottleneckBlockDesc2 (class in niftynet.network.resnet)
(class in niftynet.network.se_resnet)
BSplineFieldImageGridWarperLayer (class in niftynet.layer.spatial_transformer)
BuiltinOverlapEvaluation (class in niftynet.evaluation.segmentation_evaluations)
C
CachedFunction() (in module niftynet.utilities.util_common)
CachedFunctionByID() (in module niftynet.utilities.util_common)
CachedSubanalysisEvaluation (class in niftynet.evaluation.base_evaluations)
CachedSubanalysisEvaluator (class in niftynet.evaluation.base_evaluator)
CacheFunctionOutput (class in niftynet.utilities.util_common)
call_asm() (RegionProperties method)
call_contrast() (RegionProperties method)
call_correlation() (RegionProperties method)
call_difference_entropy() (RegionProperties method)
call_difference_variance() (RegionProperties method)
call_entropy() (RegionProperties method)
call_idifferent_moment() (RegionProperties method)
call_imc1() (RegionProperties method)
call_imc2() (RegionProperties method)
call_sum_average() (RegionProperties method)
call_sum_entropy() (RegionProperties method)
call_sum_square() (RegionProperties method)
call_sum_variance() (RegionProperties method)
candidate_indices() (in module niftynet.contrib.segmentation_selective_sampler.sampler_selective)
cauchy_1d() (in module niftynet.layer.approximated_smoothing)
centre_of_mass() (RegionProperties method)
ChannelSELayer (class in niftynet.layer.squeeze_excitation)
ChannelSparseBNLayer (class in niftynet.layer.channel_sparse_convolution)
ChannelSparseConvLayer (class in niftynet.layer.channel_sparse_convolution)
ChannelSparseConvolutionalLayer (class in niftynet.layer.channel_sparse_convolution)
ChannelSparseDeconvLayer (class in niftynet.layer.channel_sparse_convolution)
ChannelSpatialSELayer (class in niftynet.layer.squeeze_excitation)
check_binary() (PairwiseMeasures method)
check_constraint() (in module niftynet.contrib.segmentation_selective_sampler.test_sampler_selective)
check_criteria() (EarlyStopper method)
check_csv_sampler_valid() (CSVPatchSampler method)
check_divisible_channels() (in module niftynet.layer.layer_util)
check_pep_440() (in module niftynet.utilities.versioning)
check_should_stop() (in module niftynet.engine.handler_early_stopping)
check_spatial_dims() (in module niftynet.layer.layer_util)
ClassificationApplication (class in niftynet.application.classification_application)
(class in niftynet.contrib.csv_reader.classification_application)
ClassificationEvaluator (class in niftynet.evaluation.classification_evaluator)
ClassSegFinnet (class in niftynet.contrib.csv_reader.class_seg_finnet)
clear() (niftynet.application.base_application.SingletonApplication class method)
close_all() (ImageWindowDataset method)
(PairwiseResizeSampler method)
,
[1]
(PairwiseUniformSampler method)
,
[1]
close_logger() (in module niftynet.io.misc_io)
coeff_shape (GridWarperLayer attribute)
com_dist() (PairwiseMeasures method)
com_ref (class in niftynet.contrib.evaluation.segmentation_evaluations)
com_ref() (PairwiseMeasures method)
com_seg() (PairwiseMeasures method)
combine_with() (AffineWarpConstraints method)
common_bn (BottleneckBlockDesc2 attribute)
,
[1]
compactness() (RegionProperties method)
compute_generalisation_loss() (in module niftynet.engine.handler_early_stopping)
compute_orientation() (in module niftynet.io.misc_io)
ConfigStore (class in niftynet.utilities.download)
ConfigStoreCache (class in niftynet.utilities.download)
connect_data_and_network() (AutoencoderApplication method)
,
[1]
(BaseApplication method)
(ClassificationApplication method)
,
[1]
(DecayLearningRateApplication method)
(GANApplication method)
,
[1]
(ISampleRegression method)
(MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegApp method)
,
[1]
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
(SelectiveSampling method)
connected_elements() (PairwiseMeasures method)
connected_errormaps (PairwiseMeasures attribute)
ConsoleLogger (class in niftynet.engine.handler_console)
Constant (class in niftynet.engine.application_initializer)
Constraint (class in niftynet.contrib.segmentation_selective_sampler.sampler_selective)
constraints (AffineGridWarperLayer attribute)
(AffineWarpConstraints attribute)
contrast() (RegionProperties method)
conv (BottleneckBlockDesc1 attribute)
,
[1]
(BottleneckBlockDesc2 attribute)
,
[1]
conv1 (ResNetDesc attribute)
(SE_ResNetDesc attribute)
conv_shortcut (BottleneckBlockDesc2 attribute)
,
[1]
ConvDecoder (class in niftynet.network.vae)
ConvEncoder (class in niftynet.network.vae)
ConvLayer (class in niftynet.layer.convolution)
ConvolutionalLayer (class in niftynet.layer.convolution)
coordinates_placeholder() (ImageWindow method)
correct_image_if_necessary() (in module niftynet.io.misc_io)
correlation() (RegionProperties method)
cosine_loss() (in module niftynet.layer.loss_regression)
create() (BottleneckBlock method)
,
[1]
(DownResBlock method)
,
[1]
(ResNet method)
(SE_ResNet method)
(niftynet.engine.application_factory.ModuleFactory class method)
create_affine_pixdim() (in module niftynet.io.misc_io)
create_block() (DenseFeatureStackBlock method)
(DenseFeatureStackBlockWithSkipAndDownsample method)
create_graph() (ApplicationDriver static method)
create_instance() (niftynet.io.image_type.ImageFactory class method)
create_label_size_map() (in module niftynet.contrib.segmentation_selective_sampler.sampler_selective)
create_mapping_from_multimod_arrayfiles() (in module niftynet.utilities.histogram_standardisation)
create_network() (DenseVNet method)
create_probability_weights() (in module niftynet.contrib.segmentation_selective_sampler.sampler_selective)
create_standard_range() (in module niftynet.utilities.histogram_standardisation)
CRFAsRNNLayer (class in niftynet.layer.crf)
crop_batch() (ImageWindowsAggregator static method)
crop_sampling_map() (in module niftynet.contrib.csv_reader.sampler_weighted_v2_csv)
(in module niftynet.engine.sampler_weighted_v2)
CropConcat (class in niftynet.network.unet_2d)
CropLayer (class in niftynet.layer.crop)
cross_entropy() (in module niftynet.layer.loss_classification)
(in module niftynet.layer.loss_segmentation)
cross_entropy_dense() (in module niftynet.layer.loss_segmentation)
cross_entropy_function() (in module niftynet.layer.loss_gan)
csvcenter_spatial_coordinates() (CSVPatchSampler method)
CSVPatchSampler (class in niftynet.contrib.csv_reader.sampler_csvpatch)
CSVReader (class in niftynet.contrib.csv_reader.csv_reader)
current_iter (IterationMessage attribute)
current_iter_output (IterationMessage attribute)
D
damerau_levenshtein_distance() (in module niftynet.utilities.util_common)
data_feed_dict (IterationMessage attribute)
data_param (ImageSetsPartitioner attribute)
data_split_file (ImageSetsPartitioner attribute)
DataDependentLayer (class in niftynet.layer.base_layer)
DataFrameAggregator (class in niftynet.evaluation.base_evaluator)
DataFromFile (class in niftynet.io.image_type)
dataset_preprocessing() (ImageWindowDataset method)
DecayLearningRateApplication (class in niftynet.contrib.learning_rate_schedule.decay_lr_application)
decode_batch() (GridSamplesAggregator method)
(ImageWindowsAggregator method)
(ResizeSamplesAggregator method)
(WindowAsImageAggregator method)
DeconvLayer (class in niftynet.layer.deconvolution)
DeconvolutionalLayer (class in niftynet.layer.deconvolution)
DeepMedic (class in niftynet.network.deepmedic)
default_b_initializer() (in module niftynet.layer.convolution)
(in module niftynet.layer.deconvolution)
(in module niftynet.layer.fully_connected)
default_evaluation_list() (BaseEvaluator method)
(ClassificationEvaluator method)
(RegressionEvaluator method)
(SegmentationEvaluator method)
default_image_file_location (ImageSetsPartitioner attribute)
default_w_initializer() (in module niftynet.layer.convolution)
(in module niftynet.layer.deconvolution)
(in module niftynet.layer.fully_connected)
DenseFeatureStackBlock (class in niftynet.network.dense_vnet)
DenseFeatureStackBlockWithSkipAndDownsample (class in niftynet.network.dense_vnet)
DenseVNet (class in niftynet.network.dense_vnet)
detection_error() (PairwiseMeasures method)
device_string() (in module niftynet.utilities.util_common)
dice (class in niftynet.evaluation.segmentation_evaluations)
Dice (in module niftynet.evaluation.segmentation_evaluations)
dice() (in module niftynet.layer.loss_segmentation)
dice_dense() (in module niftynet.layer.loss_segmentation)
dice_dense_nosquare() (in module niftynet.layer.loss_segmentation)
dice_nosquare() (in module niftynet.layer.loss_segmentation)
dice_plus_xent_loss() (in module niftynet.layer.loss_segmentation)
dice_score() (PairwiseMeasures method)
difference_variance_entropy() (RegionProperties method)
DilatedTensor (class in niftynet.layer.dilatedcontext)
DiscreteLabelNormalisationLayer (class in niftynet.layer.discrete_label_normalisation)
do_reorientation() (in module niftynet.io.misc_io)
do_reorientation_idx() (in module niftynet.io.misc_io)
do_resampling() (in module niftynet.io.misc_io)
do_resampling_idx() (in module niftynet.io.misc_io)
do_setup() (in module versioneer)
do_vcs_install() (in module versioneer)
DownBlock (class in niftynet.layer.downsample_res_block)
download() (in module niftynet.utilities.download)
download_and_decompress() (in module niftynet.utilities.download)
download_file() (in module niftynet.utilities.download)
DownResBlock (class in niftynet.network.resnet)
(class in niftynet.network.se_resnet)
DownResBlockDesc (class in niftynet.network.resnet)
(class in niftynet.network.se_resnet)
DownSampleLayer (class in niftynet.layer.downsample)
dtype (DataFromFile attribute)
(SpatialImage2D attribute)
dtype_casting() (in module niftynet.io.misc_io)
dummy_coordinates() (niftynet.engine.image_window_dataset.ImageWindowDataset class method)
E
EarlyStopper (class in niftynet.engine.handler_early_stopping)
ElementwiseLayer (class in niftynet.layer.elementwise)
energy() (RegionProperties method)
entropy() (RegionProperties method)
ErrorMapsCC (class in niftynet.contrib.evaluation.segmentation_evaluations)
evaluate() (BaseEvaluator method)
evaluate_from_generator() (BaseEvaluator method)
evaluate_next() (BaseEvaluator method)
(CachedSubanalysisEvaluator method)
EvaluationApplicationDriver (class in niftynet.evaluation.evaluation_application_driver)
EvaluationFactory (class in niftynet.engine.application_factory)
EventHandlerFactory (class in niftynet.engine.application_factory)
exists() (ConfigStore method)
(ConfigStoreCache method)
(RemoteConfigStore method)
(RemoteProxy method)
expand_spatial_params() (in module niftynet.layer.layer_util)
expand_to_5d() (in module niftynet.io.misc_io)
F
false_positive_rate (class in niftynet.evaluation.segmentation_evaluations)
false_positive_rate() (PairwiseMeasures method)
fc (ResNetDesc attribute)
(SE_ResNetDesc attribute)
FCDecoder (class in niftynet.network.vae)
FCLayer (class in niftynet.layer.fully_connected)
file_path (DataFromFile attribute)
finalise_output_op() (OutputsCollector method)
find_set_of_labels() (in module niftynet.layer.discrete_label_normalisation)
float_array() (in module niftynet.utilities.user_parameters_helper)
fn (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
foreground_component() (MorphologyOps method)
fp (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
from_data_reader_properties() (niftynet.engine.image_window.ImageWindow class method)
from_dict() (niftynet.utilities.filename_matching.KeywordsMatching class method)
ftheta() (in module niftynet.layer.crf)
FullyConnectedLayer (class in niftynet.layer.fully_connected)
G
GANApplication (class in niftynet.application.gan_application)
(class in niftynet.contrib.csv_reader.applications_maybe.gan_application)
GANImageBlock (class in niftynet.layer.gan_blocks)
gaussian_1d() (in module niftynet.layer.approximated_smoothing)
GaussianSampler (class in niftynet.network.vae)
generalised_dice_loss() (in module niftynet.layer.loss_segmentation)
generalised_wasserstein_dice_loss() (in module niftynet.layer.loss_segmentation)
GenericGAN (class in niftynet.network.simple_gan)
get_2d_reader() (in module niftynet.contrib.segmentation_selective_sampler.test_sampler_selective)
get_3d_reader() (in module niftynet.contrib.segmentation_selective_sampler.test_sampler_selective)
get_aggregations() (accuracy method)
(BaseEvaluation method)
(PerComponentScalarEvaluation method)
(roc method)
(roc_auc method)
get_cmdclass() (in module versioneer)
get_config() (in module niftynet.utilities.versioneer_version)
get_config_from_root() (in module versioneer)
get_data() (DataFromFile method)
(Loadable method)
(SpatialImage2D method)
(SpatialImage4D method)
get_default_examples_folder() (NiftyNetGlobalConfig method)
get_download_params() (ConfigStoreCache method)
(RemoteProxy method)
get_download_server_url() (NiftyNetGlobalConfig method)
get_dynamic_window_reader() (in module niftynet.contrib.segmentation_selective_sampler.test_sampler_selective)
get_file_list() (ImageSetsPartitioner method)
get_file_lists_by() (ImageSetsPartitioner method)
get_image_index() (ImageReader method)
get_initializer() (InitializerFactory static method)
get_instance() (Adagrad static method)
(Adam static method)
(Constant static method)
(GlorotNormal static method)
(GlorotUniform static method)
(GradientDescent static method)
(HeNormal static method)
(HeUniform static method)
(Momentum static method)
(NesterovMomentum static method)
(Ones static method)
(Orthogonal static method)
(RMSProp static method)
(UniformUnitScaling static method)
(VarianceScaling static method)
(Zeros static method)
get_keywords() (in module niftynet.utilities.versioneer_version)
get_latest_subfolder() (in module niftynet.io.misc_io)
get_local_cache_folder() (ConfigStoreCache method)
get_local_path() (ConfigStoreCache method)
(RemoteProxy method)
get_niftynet_config_folder() (NiftyNetGlobalConfig method)
get_niftynet_home_folder() (NiftyNetGlobalConfig method)
get_niftynet_version() (in module niftynet.utilities.versioning)
get_niftynet_version_string() (in module niftynet.utilities.versioning)
get_pairwise_inputs() (PairwiseResizeSampler method)
,
[1]
(PairwiseUniformSampler method)
,
[1]
get_relative_corners() (in module niftynet.layer.affine_augmentation)
get_root() (in module versioneer)
get_sampler() (BaseApplication method)
get_subject() (ImageReader method)
get_subject_id() (ImageReader method)
get_url() (RemoteConfigStore method)
get_version() (in module versioneer)
get_versions() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
git_get_keywords() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
git_pieces_from_vcs() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
git_versions_from_keywords() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
glcm() (RegionProperties method)
global_section (NiftyNetGlobalConfig attribute)
global_vars_init_or_restore() (in module niftynet.engine.application_variables)
GlorotNormal (class in niftynet.engine.application_initializer)
GlorotUniform (class in niftynet.engine.application_initializer)
GNLayer (class in niftynet.layer.gn)
gradient_op (BaseApplication attribute)
GradientDescent (class in niftynet.engine.application_optimiser)
gradients (GradientsCollector attribute)
gradients_collector (BaseApplication attribute)
GradientsCollector (class in niftynet.engine.application_variables)
GRAPH_CREATED (in module niftynet.engine.signal)
grep_files_by_data_section() (ImageSetsPartitioner method)
grid_spatial_coordinates() (in module niftynet.contrib.csv_reader.sampler_grid_v2_csv)
(in module niftynet.engine.sampler_grid_v2)
GridSampler (class in niftynet.engine.sampler_grid_v2)
GridSamplerCSV (class in niftynet.contrib.csv_reader.sampler_grid_v2_csv)
GridSamplesAggregator (class in niftynet.engine.windows_aggregator_grid)
GridWarperLayer (class in niftynet.layer.grid_warper)
H
harilick() (RegionProperties method)
harilick_matrix() (RegionProperties method)
has_bad_inputs() (in module niftynet.utilities.util_common)
has_inference (ImageSetsPartitioner attribute)
has_phase() (ImageSetsPartitioner method)
has_section_in_config() (in module niftynet.utilities.user_parameters_helper)
has_training (ImageSetsPartitioner attribute)
has_validation (ImageSetsPartitioner attribute)
hausdorff95_distance (class in niftynet.evaluation.segmentation_evaluations)
hausdorff_distance (class in niftynet.evaluation.segmentation_evaluations)
header_str() (PairwiseMeasures method)
(PairwiseMeasuresRegression method)
(RegionProperties method)
HeNormal (class in niftynet.engine.application_initializer)
HeUniform (class in niftynet.engine.application_initializer)
HighRes3DNet (class in niftynet.network.highres3dnet)
HighRes3DNetFeatures (class in niftynet.contrib.csv_reader.highres3dnet_features)
HighRes3DNetLarge (class in niftynet.network.highres3dnet_large)
HighRes3DNetSmall (class in niftynet.network.highres3dnet_small)
HighResBlock (class in niftynet.contrib.csv_reader.highres3dnet_features)
(class in niftynet.network.highres3dnet)
HistogramNormalisationLayer (class in niftynet.layer.histogram_normalisation)
HolisticNet (class in niftynet.network.holistic_net)
home_key (NiftyNetGlobalConfig attribute)
homogeneity() (RegionProperties method)
huber_loss() (in module niftynet.layer.loss_regression)
I
image2nibabel() (in module niftynet.io.image_loader)
image3() (in module niftynet.io.misc_io)
image3_axial() (in module niftynet.io.misc_io)
image3_coronal() (in module niftynet.io.misc_io)
image3_sagittal() (in module niftynet.io.misc_io)
image_data_placeholder() (ImageWindow method)
image_id (ImageWindowsAggregator attribute)
ImageAsNibabel (class in niftynet.io.image_loader)
ImageDiscriminator (class in niftynet.contrib.ultrasound_simulator_gan.ultrasound_simulator_gan)
(class in niftynet.network.simple_gan)
(class in niftynet.network.simulator_gan)
ImageFactory (class in niftynet.io.image_type)
ImageGenerator (class in niftynet.contrib.ultrasound_simulator_gan.ultrasound_simulator_gan)
(class in niftynet.network.simple_gan)
(class in niftynet.network.simulator_gan)
ImageReader (class in niftynet.io.image_reader)
ImageSetsPartitioner (class in niftynet.io.image_sets_partitioner)
ImageWindow (class in niftynet.engine.image_window)
ImageWindowDataset (class in niftynet.engine.image_window_dataset)
ImageWindowDatasetCSV (class in niftynet.contrib.csv_reader.sampler_csv_rows)
ImageWindowsAggregator (class in niftynet.engine.windows_aggregator_base)
imread_nibabel() (in module niftynet.io.image_loader)
imread_numpy() (in module niftynet.io.image_loader)
imread_opencv() (in module niftynet.io.image_loader)
imread_pillow() (in module niftynet.io.image_loader)
imread_sitk() (in module niftynet.io.image_loader)
imread_skimage() (in module niftynet.io.image_loader)
INetAffine (class in niftynet.network.interventional_affine_net)
INetDense (class in niftynet.network.interventional_dense_net)
INetHybridPreWarp (class in niftynet.network.interventional_hybrid_net)
INetHybridTwoStream (class in niftynet.network.interventional_hybrid_net)
infer_latest_model_file() (in module niftynet.io.misc_io)
infer_ndims_from_file() (in module niftynet.io.misc_io)
infer_output_dims() (in module niftynet.layer.deconvolution)
infer_spatial_rank() (in module niftynet.layer.layer_util)
infer_tf_dtypes() (in module niftynet.io.image_reader)
inference_files (ImageSetsPartitioner attribute)
information_measure_correlation() (RegionProperties method)
informedness (class in niftynet.evaluation.segmentation_evaluations)
informedness() (PairwiseMeasures method)
init_affine_b() (in module niftynet.network.interventional_affine_net)
init_affine_w() (in module niftynet.network.interventional_affine_net)
init_dataset() (ImageWindowDataset method)
init_non_uniform_angle() (RandomRotationLayer method)
init_order() (RandomBiasFieldLayer method)
init_saver() (ModelSaver method)
init_uniform_angle() (RandomRotationLayer method)
init_uniform_coeff() (RandomBiasFieldLayer method)
init_writer() (TensorBoardLogger method)
initialise() (CSVReader method)
(ImageReader method)
(ImageSetsPartitioner method)
initialise_aggregator() (ClassificationApplication method)
,
[1]
(MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegressionApplication method)
,
[1]
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
initialise_application() (ApplicationDriver method)
(EvaluationApplicationDriver method)
initialise_balanced_sampler() (MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
initialise_classifier_aggregator() (MultiOutputApplication method)
initialise_csvsampler() (SegmentationApplicationPatchSampler method)
initialise_dataset_loader() (AutoencoderApplication method)
,
[1]
(BaseApplication method)
(ClassificationApplication method)
,
[1]
(GANApplication method)
,
[1]
(ISampleRegression method)
(MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegApp method)
,
[1]
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationBFAug method)
(SegmentationApplicationPatchSampler method)
(SelectiveSampling method)
initialise_evaluator() (ClassificationApplication method)
,
[1]
(MultiClassifSegApplication method)
(RegressionApplication method)
,
[1]
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
initialise_grid_aggregator() (MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
(SelectiveSampling method)
initialise_grid_sampler() (MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
(SelectiveSampling method)
initialise_identity_aggregator() (MultiOutputApplication method)
(RegressionApplication method)
initialise_network() (AutoencoderApplication method)
,
[1]
(BaseApplication method)
(ClassificationApplication method)
,
[1]
(GANApplication method)
,
[1]
(MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegApp method)
,
[1]
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
(SelectiveSampling method)
initialise_resize_aggregator() (MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
initialise_resize_sampler() (ClassificationApplication method)
,
[1]
(MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
initialise_sampler() (AutoencoderApplication method)
,
[1]
(BaseApplication method)
(ClassificationApplication method)
,
[1]
(GANApplication method)
,
[1]
(MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegApp method)
,
[1]
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
(SelectiveSampling method)
initialise_selective_sampler() (SelectiveSampling method)
initialise_uniform_sampler() (MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
initialise_weighted_sampler() (MultiClassifSegApplication method)
(MultiOutputApplication method)
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
InitializerFactory (class in niftynet.engine.application_factory)
initializers (TrainableLayer attribute)
input_image (ImageWindowsAggregator attribute)
input_sources (ImageReader attribute)
INSTANCE_DICT (ImageFactory attribute)
InstanceNormLayer (class in niftynet.layer.bn)
int_array() (in module niftynet.utilities.user_parameters_helper)
interp_order (SpatialImage2D attribute)
interpret_output() (AutoencoderApplication method)
,
[1]
(BaseApplication method)
(ClassificationApplication method)
,
[1]
(GANApplication method)
,
[1]
(MultiClassifSegApplication method)
(MultiOutputApplication method)
(OutputInterpreter method)
(RegApp method)
,
[1]
(RegressionApplication method)
,
[1]
(RegressionRecApplication method)
(SegmentationApplication method)
,
[1]
(SegmentationApplicationPatchSampler method)
(SelectiveSampling method)
intersection_over_union (in module niftynet.evaluation.segmentation_evaluations)
intersection_over_union() (PairwiseMeasures method)
inverse() (AffineAugmentationLayer method)
inverse_difference_moment() (RegionProperties method)
inverse_op() (AffineGridWarperLayer method)
(DiscreteLabelNormalisationLayer method)
(Invertible method)
(PadLayer method)
Invertible (class in niftynet.layer.base_layer)
is_evaluation (BaseApplication attribute)
is_inference (BaseApplication attribute)
(IterationMessage attribute)
is_ready() (DataDependentLayer method)
(DiscreteLabelNormalisationLayer method)
(HistogramNormalisationLayer method)
is_training (BaseApplication attribute)
(IterationMessage attribute)
is_validation (BaseApplication attribute)
(IterationMessage attribute)
ISampleRegression (class in niftynet.contrib.regression_weighted_sampler.isample_regression)
iter_duration (IterationMessage attribute)
ITER_FINISHED (in module niftynet.engine.signal)
ITER_STARTED (in module niftynet.engine.signal)
IterationMessage (class in niftynet.engine.application_iteration)
IterationMessageGenerator (class in niftynet.engine.application_iteration)
IteratorFactory (class in niftynet.engine.application_factory)
J
jaccard (class in niftynet.evaluation.segmentation_evaluations)
Jaccard (in module niftynet.evaluation.segmentation_evaluations)
jaccard() (PairwiseMeasures method)
join_subject_id_and_filename_list() (in module niftynet.utilities.util_csv)
K
key (DiscreteLabelNormalisationLayer attribute)
KeywordsMatching (class in niftynet.utilities.filename_matching)
kurtosis_() (RegionProperties method)
L
l1_loss() (in module niftynet.layer.loss_regression)
l2_loss() (in module niftynet.layer.loss_regression)
labels_to_one_hot() (in module niftynet.layer.loss_classification_multi)
(in module niftynet.layer.loss_segmentation)
Layer (class in niftynet.layer.base_layer)
layer_op() (accuracy method)
(ActiLayer method)
(AdditiveUpsampleLayer method)
(AffineAugmentationLayer method)
(AffineGridWarperLayer method)
(BNLayer method)
(BSplineFieldImageGridWarperLayer method)
(BaseEvaluation method)
(BaseRegressionEvaluation method)
(BinaryMaskingLayer method)
(BottleneckBlock method)
,
[1]
(CRFAsRNNLayer method)
(CSVPatchSampler method)
(CSVReader method)
(CachedSubanalysisEvaluation method)
(ChannelSELayer method)
(ChannelSparseBNLayer method)
(ChannelSparseConvLayer method)
(ChannelSparseConvolutionalLayer method)
(ChannelSparseDeconvLayer method)
(ChannelSpatialSELayer method)
(ClassSegFinnet method)
(ConvDecoder method)
(ConvEncoder method)
(ConvLayer method)
(ConvolutionalLayer method)
(CropConcat method)
(CropLayer method)
(DeconvLayer method)
(DeconvolutionalLayer method)
(DeepMedic method)
(DenseFeatureStackBlock method)
(DenseFeatureStackBlockWithSkipAndDownsample method)
(DenseVNet method)
(DiscreteLabelNormalisationLayer method)
(DownBlock method)
(DownResBlock method)
,
[1]
(DownSampleLayer method)
(ElementwiseLayer method)
(ErrorMapsCC method)
(FCDecoder method)
(FCLayer method)
(FullyConnectedLayer method)
(GANImageBlock method)
(GNLayer method)
(GaussianSampler method)
(GenericGAN method)
(GridSampler method)
(GridSamplerCSV method)
(GridWarperLayer method)
(HighRes3DNet method)
(HighRes3DNetFeatures method)
(HighRes3DNetLarge method)
(HighRes3DNetSmall method)
(HighResBlock method)
,
[1]
(HistogramNormalisationLayer method)
(HolisticNet method)
(INetAffine method)
(INetDense method)
(INetHybridPreWarp method)
(INetHybridTwoStream method)
(ImageDiscriminator method)
,
[1]
,
[2]
(ImageGenerator method)
,
[1]
,
[2]
(ImageReader method)
(ImageWindowDataset method)
(ImageWindowDatasetCSV method)
(InstanceNormLayer method)
(Layer method)
(LayerFromCallable method)
(LinearInterpolateSampler method)
(LinearInterpolateSamplerCSV method)
(LinearResizeLayer method)
(LossFunction method)
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
(MeanVarNormalisationLayer method)
(MergeLayer method)
(PadLayer method)
(PairwiseResizeSampler method)
,
[1]
(PairwiseUniformSampler method)
,
[1]
(PerComponentEvaluation method)
(PostProcessingLayer method)
(RGBHistogramEquilisationLayer method)
(RandomBiasFieldLayer method)
(RandomElasticDeformationLayer method)
(RandomFlipLayer method)
(RandomRotationLayer method)
(RandomSpatialScalingLayer method)
(RandomVectorSampler method)
,
[1]
(ResNet method)
(ResampledFieldGridWarperLayer method)
(ResamplerLayer method)
(RescaledFieldImageGridWarperLayer method)
(ResidualUnit method)
(ResidualUpsampleLayer method)
(ResizeSampler method)
(ResizeSamplerCSV method)
(SE_ResNet method)
(ScaleBlock method)
(ScaleNet method)
(ScoreLayer method)
(SmoothingLayer method)
(SpatialGradientLayer method)
(SpatialPriorBlock method)
(SpatialSELayer method)
(SubPixelLayer method)
(ToyNet method)
(ToyNetFeat method)
(TwoLayerConv method)
(UNet2D method)
(UNet3D method)
,
[1]
(UNetBlock method)
,
[1]
(UniformSampler method)
(UniformSamplerCSV method)
(UpBlock method)
(UpSampleLayer method)
(VAE method)
(VNet method)
(VNetBlock method)
(roc method)
(roc_auc method)
layer_scope() (Layer method)
LayerFromCallable (class in niftynet.layer.base_layer)
leaky_relu() (in module niftynet.layer.activation)
LinearInterpolateSampler (class in niftynet.engine.sampler_linear_interpolate_v2)
LinearInterpolateSamplerCSV (class in niftynet.contrib.csv_reader.sampler_linear_interpolate_v2_csv)
LinearResizeLayer (class in niftynet.layer.linear_resize)
list_depth_count() (in module niftynet.utilities.util_common)
list_labels() (PairwiseMeasures method)
load_data_sections_by_subject() (ImageSetsPartitioner method)
load_event_handlers() (ApplicationDriver method)
load_image_obj() (in module niftynet.io.image_loader)
Loadable (class in niftynet.io.image_type)
loader (DataFromFile attribute)
log_inferred() (ImageWindowsAggregator method)
look_up_operations() (in module niftynet.utilities.util_common)
loop() (ApplicationDriver static method)
loop_step() (ApplicationDriver static method)
loss_confusion_matrix() (in module niftynet.layer.loss_classification_multi)
loss_variability() (in module niftynet.layer.loss_classification_multi)
LossAutoencoderFactory (class in niftynet.engine.application_factory)
LossClassificationFactory (class in niftynet.engine.application_factory)
LossClassificationMultiFactory (class in niftynet.engine.application_factory)
LossFunction (class in niftynet.layer.loss_autoencoder)
(class in niftynet.layer.loss_classification)
(class in niftynet.layer.loss_classification_multi)
(class in niftynet.layer.loss_gan)
(class in niftynet.layer.loss_regression)
(class in niftynet.layer.loss_segmentation)
LossGANFactory (class in niftynet.engine.application_factory)
LossRegressionFactory (class in niftynet.engine.application_factory)
LossSegmentationFactory (class in niftynet.engine.application_factory)
M
mae (class in niftynet.evaluation.regression_evaluations)
mae() (PairwiseMeasuresRegression method)
mae_loss() (in module niftynet.layer.loss_regression)
main() (in module niftynet)
(in module niftynet.contrib.checkpoint_tools.rename_checkpoint_to_partial)
(in module niftynet.utilities.download)
make_affine_from_sitk() (in module niftynet.io.image_loader)
make_callable_loss_func() (LossFunction method)
,
[1]
,
[2]
,
[3]
make_gradients_op() (ApplyGradients method)
make_input_tuple() (in module niftynet.utilities.user_parameters_helper)
make_model_name() (in module niftynet.engine.handler_model)
markedness (class in niftynet.evaluation.segmentation_evaluations)
markedness() (PairwiseMeasures method)
match_and_write_filenames_to_csv() (in module niftynet.utilities.util_csv)
match_array() (in module niftynet.utilities.user_parameters_regex)
match_first_degree() (in module niftynet.utilities.util_csv)
match_image_shapes() (ImageWindow method)
match_second_degree() (in module niftynet.utilities.util_csv)
matching_subjects_and_filenames() (KeywordsMatching method)
max_() (RegionProperties method)
mean_() (RegionProperties method)
MeanVarNormalisationLayer (class in niftynet.layer.mean_variance_normalisation)
measured_average_distance() (PairwiseMeasures method)
measured_distance() (PairwiseMeasures method)
measured_hausdorff_distance() (PairwiseMeasures method)
median_() (RegionProperties method)
MergeLayer (class in niftynet.network.holistic_net)
metric() (BaseRegressionEvaluation method)
(mae method)
(mse method)
(rmse method)
metric_dict_from_binarized() (PerComponentEvaluation method)
(PerComponentScalarEvaluation method)
metric_from_binarized() (average_distance method)
(BuiltinOverlapEvaluation method)
(PerComponentScalarEvaluation method)
(com_ref method)
(hausdorff95_distance method)
(hausdorff_distance method)
metric_from_confusion_matrix() (accuracy method)
(BuiltinOverlapEvaluation method)
(dice method)
(false_positive_rate method)
(fn method)
(fp method)
(informedness method)
(jaccard method)
(markedness method)
(n_intersection method)
(n_neg_ref method)
(n_neg_seg method)
(n_pos_ref method)
(n_pos_seg method)
(n_union method)
(negative_predictive_values method)
(positive_predictive_values method)
(sensitivity method)
(specificity method)
(tn method)
(tp method)
(vol_diff method)
min_() (RegionProperties method)
min_number_from_ratio() (Constraint method)
mode (BaseApplication attribute)
ModelRestorer (class in niftynet.engine.handler_model)
ModelSaver (class in niftynet.engine.handler_model)
ModuleFactory (class in niftynet.engine.application_factory)
Momentum (class in niftynet.engine.application_optimiser)
MorphologyOps (class in niftynet.utilities.util_common)
mse (class in niftynet.evaluation.regression_evaluations)
mse() (PairwiseMeasuresRegression method)
MultiClassifSegApplication (class in niftynet.contrib.csv_reader.multitask_classifseg_application)
MultiOutputApplication (class in niftynet.contrib.multi_output.multi_output_test)
N
n_intersection (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
n_neg_ref (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
n_neg_seg (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
n_pos_ref (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
n_pos_seg (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
n_union (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
name (DataFromFile attribute)
names (ImageReader attribute)
(ImageWindow attribute)
negative_predictive_values (class in niftynet.evaluation.segmentation_evaluations)
negative_predictive_values() (PairwiseMeasures method)
NesterovMomentum (class in niftynet.engine.application_optimiser)
net (BaseApplication attribute)
new_partition (ImageSetsPartitioner attribute)
NIFTYNET (in module niftynet.engine.signal)
niftynet (module)
,
[1]
niftynet.application (module)
,
[1]
niftynet.application.autoencoder_application (module)
niftynet.application.base_application (module)
niftynet.application.classification_application (module)
niftynet.application.gan_application (module)
niftynet.application.label_driven_registration (module)
niftynet.application.regression_application (module)
niftynet.application.segmentation_application (module)
niftynet.contrib (module)
,
[1]
niftynet.contrib.checkpoint_tools (module)
niftynet.contrib.checkpoint_tools.rename_checkpoint_to_partial (module)
niftynet.contrib.csv_reader (module)
niftynet.contrib.csv_reader.applications_maybe (module)
niftynet.contrib.csv_reader.applications_maybe.autoencoder_application (module)
niftynet.contrib.csv_reader.applications_maybe.gan_application (module)
niftynet.contrib.csv_reader.applications_maybe.label_driven_registration (module)
niftynet.contrib.csv_reader.applications_maybe.regression_application (module)
niftynet.contrib.csv_reader.applications_maybe.segmentation_application (module)
niftynet.contrib.csv_reader.class_seg_finnet (module)
niftynet.contrib.csv_reader.classification_application (module)
niftynet.contrib.csv_reader.csv_reader (module)
niftynet.contrib.csv_reader.highres3dnet_features (module)
niftynet.contrib.csv_reader.multitask_classifseg_application (module)
niftynet.contrib.csv_reader.sampler_balanced_v2_csv (module)
niftynet.contrib.csv_reader.sampler_csv_rows (module)
niftynet.contrib.csv_reader.sampler_csvpatch (module)
niftynet.contrib.csv_reader.sampler_grid_v2_csv (module)
niftynet.contrib.csv_reader.sampler_linear_interpolate_v2_csv (module)
niftynet.contrib.csv_reader.sampler_random_vector_v2_csv (module)
niftynet.contrib.csv_reader.sampler_resize_v2_csv (module)
niftynet.contrib.csv_reader.sampler_uniform_v2_csv (module)
niftynet.contrib.csv_reader.sampler_weighted_v2_csv (module)
niftynet.contrib.csv_reader.segmentation_application_patchsampler (module)
niftynet.contrib.csv_reader.toynet_features (module)
niftynet.contrib.deep_boosted_regression (module)
niftynet.contrib.deep_boosted_regression.regression_rec_application (module)
niftynet.contrib.evaluation (module)
niftynet.contrib.evaluation.classification_evaluations (module)
niftynet.contrib.evaluation.regression_evaluations (module)
niftynet.contrib.evaluation.segmentation_evaluations (module)
niftynet.contrib.layer (module)
niftynet.contrib.layer.resampler_optional_niftyreg (module)
niftynet.contrib.learning_rate_schedule (module)
niftynet.contrib.learning_rate_schedule.decay_lr_application (module)
niftynet.contrib.multi_output (module)
niftynet.contrib.multi_output.multi_output_test (module)
niftynet.contrib.niftyreg_image_resampling (module)
niftynet.contrib.niftyreg_image_resampling.tests (module)
niftynet.contrib.preprocessors (module)
niftynet.contrib.preprocessors.preprocessing (module)
niftynet.contrib.regression_weighted_sampler (module)
niftynet.contrib.regression_weighted_sampler.isample_regression (module)
niftynet.contrib.sampler_pairwise (module)
niftynet.contrib.sampler_pairwise.sampler_pairwise_resize (module)
niftynet.contrib.sampler_pairwise.sampler_pairwise_resize_csv (module)
niftynet.contrib.sampler_pairwise.sampler_pairwise_uniform (module)
niftynet.contrib.sampler_pairwise.sampler_pairwise_uniform_csv (module)
niftynet.contrib.segmentation_bf_aug (module)
niftynet.contrib.segmentation_bf_aug.segmentation_application_bfaug (module)
niftynet.contrib.segmentation_selective_sampler (module)
niftynet.contrib.segmentation_selective_sampler.sampler_selective (module)
niftynet.contrib.segmentation_selective_sampler.ss_app (module)
niftynet.contrib.segmentation_selective_sampler.test_sampler_selective (module)
niftynet.contrib.ultrasound_simulator_gan (module)
niftynet.contrib.ultrasound_simulator_gan.ultrasound_simulator_gan (module)
niftynet.engine (module)
,
[1]
niftynet.engine.application_driver (module)
niftynet.engine.application_factory (module)
niftynet.engine.application_initializer (module)
niftynet.engine.application_iteration (module)
niftynet.engine.application_optimiser (module)
niftynet.engine.application_variables (module)
niftynet.engine.handler_console (module)
niftynet.engine.handler_early_stopping (module)
niftynet.engine.handler_gradient (module)
niftynet.engine.handler_model (module)
niftynet.engine.handler_network_output (module)
niftynet.engine.handler_performance (module)
niftynet.engine.handler_sampler (module)
niftynet.engine.handler_tensorboard (module)
niftynet.engine.image_window (module)
niftynet.engine.image_window_dataset (module)
niftynet.engine.sampler_balanced_v2 (module)
niftynet.engine.sampler_grid_v2 (module)
niftynet.engine.sampler_linear_interpolate_v2 (module)
niftynet.engine.sampler_random_vector_v2 (module)
niftynet.engine.sampler_resize_v2 (module)
niftynet.engine.sampler_uniform_v2 (module)
niftynet.engine.sampler_weighted_v2 (module)
niftynet.engine.signal (module)
niftynet.engine.windows_aggregator_base (module)
niftynet.engine.windows_aggregator_grid (module)
niftynet.engine.windows_aggregator_identity (module)
niftynet.engine.windows_aggregator_resize (module)
niftynet.evaluation (module)
,
[1]
niftynet.evaluation.base_evaluations (module)
niftynet.evaluation.base_evaluator (module)
niftynet.evaluation.classification_evaluations (module)
niftynet.evaluation.classification_evaluator (module)
niftynet.evaluation.evaluation_application_driver (module)
niftynet.evaluation.pairwise_measures (module)
niftynet.evaluation.region_properties (module)
niftynet.evaluation.regression_evaluations (module)
niftynet.evaluation.regression_evaluator (module)
niftynet.evaluation.segmentation_evaluations (module)
niftynet.evaluation.segmentation_evaluator (module)
niftynet.io (module)
,
[1]
niftynet.io.image_loader (module)
niftynet.io.image_reader (module)
niftynet.io.image_sets_partitioner (module)
niftynet.io.image_type (module)
niftynet.io.misc_io (module)
niftynet.layer (module)
,
[1]
niftynet.layer.activation (module)
niftynet.layer.additive_upsample (module)
niftynet.layer.affine_augmentation (module)
niftynet.layer.approximated_smoothing (module)
niftynet.layer.base_layer (module)
niftynet.layer.binary_masking (module)
niftynet.layer.bn (module)
niftynet.layer.channel_sparse_convolution (module)
niftynet.layer.convolution (module)
niftynet.layer.crf (module)
niftynet.layer.crop (module)
niftynet.layer.deconvolution (module)
niftynet.layer.dilatedcontext (module)
niftynet.layer.discrete_label_normalisation (module)
niftynet.layer.downsample (module)
niftynet.layer.downsample_res_block (module)
niftynet.layer.elementwise (module)
niftynet.layer.fully_connected (module)
niftynet.layer.gan_blocks (module)
niftynet.layer.gn (module)
niftynet.layer.grid_warper (module)
niftynet.layer.histogram_normalisation (module)
niftynet.layer.layer_util (module)
niftynet.layer.linear_resize (module)
niftynet.layer.loss_autoencoder (module)
niftynet.layer.loss_classification (module)
niftynet.layer.loss_classification_multi (module)
niftynet.layer.loss_gan (module)
niftynet.layer.loss_regression (module)
niftynet.layer.loss_segmentation (module)
niftynet.layer.mean_variance_normalisation (module)
niftynet.layer.pad (module)
niftynet.layer.post_processing (module)
niftynet.layer.rand_bias_field (module)
niftynet.layer.rand_elastic_deform (module)
niftynet.layer.rand_flip (module)
niftynet.layer.rand_rotation (module)
niftynet.layer.rand_spatial_scaling (module)
niftynet.layer.resampler (module)
niftynet.layer.residual_unit (module)
niftynet.layer.rgb_histogram_equilisation (module)
niftynet.layer.spatial_gradient (module)
niftynet.layer.spatial_transformer (module)
niftynet.layer.squeeze_excitation (module)
niftynet.layer.subpixel (module)
niftynet.layer.upsample (module)
niftynet.layer.upsample_res_block (module)
niftynet.network (module)
,
[1]
niftynet.network.base_net (module)
niftynet.network.deepmedic (module)
niftynet.network.dense_vnet (module)
niftynet.network.highres3dnet (module)
niftynet.network.highres3dnet_large (module)
niftynet.network.highres3dnet_small (module)
niftynet.network.holistic_net (module)
niftynet.network.interventional_affine_net (module)
niftynet.network.interventional_dense_net (module)
niftynet.network.interventional_hybrid_net (module)
niftynet.network.no_new_net (module)
niftynet.network.resnet (module)
niftynet.network.scalenet (module)
niftynet.network.se_resnet (module)
niftynet.network.simple_gan (module)
niftynet.network.simulator_gan (module)
niftynet.network.toynet (module)
niftynet.network.unet (module)
niftynet.network.unet_2d (module)
niftynet.network.vae (module)
niftynet.network.vnet (module)
niftynet.utilities (module)
,
[1]
niftynet.utilities.decorators (module)
niftynet.utilities.download (module)
niftynet.utilities.filename_matching (module)
niftynet.utilities.histogram_standardisation (module)
niftynet.utilities.niftynet_global_config (module)
niftynet.utilities.niftynet_launch_config (module)
niftynet.utilities.restore_initializer (module)
niftynet.utilities.user_parameters_custom (module)
niftynet.utilities.user_parameters_default (module)
niftynet.utilities.user_parameters_helper (module)
niftynet.utilities.user_parameters_parser (module)
niftynet.utilities.user_parameters_regex (module)
niftynet.utilities.util_common (module)
niftynet.utilities.util_csv (module)
niftynet.utilities.util_import (module)
niftynet.utilities.versioneer_version (module)
niftynet.utilities.versioning (module)
niftynet_exts (NiftyNetGlobalConfig attribute)
NiftyNetGlobalConfig (class in niftynet.utilities.niftynet_global_config)
NiftyNetLaunchConfig (class in niftynet.utilities.niftynet_launch_config)
no_constraints() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
no_shear_2d() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
no_shear_3d() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
NotThisMethod
,
[1]
num_dim (AffineWarpConstraints attribute)
num_free_params (AffineWarpConstraints attribute)
num_output_channels() (PostProcessingLayer method)
num_subjects (ImageReader attribute)
num_trainable_params() (TrainableLayer method)
number_of_subjects() (ImageSetsPartitioner method)
O
Ones (class in niftynet.engine.application_initializer)
ops_to_run (IterationMessage attribute)
optimiser (BaseApplication attribute)
OptimiserFactory (class in niftynet.engine.application_factory)
original_affine (SpatialImage2D attribute)
original_axcodes (SpatialImage2D attribute)
original_pixdim (SpatialImage2D attribute)
original_shape (SpatialImage2D attribute)
Orthogonal (class in niftynet.engine.application_initializer)
otsu_threshold() (in module niftynet.utilities.util_common)
outline_error() (PairwiseMeasures method)
output_axcodes (SpatialImage2D attribute)
(SpatialImage3D attribute)
output_decoder (BaseApplication attribute)
output_pixdim (SpatialImage2D attribute)
(SpatialImage3D attribute)
output_shape (GridWarperLayer attribute)
OutputInterpreter (class in niftynet.engine.handler_network_output)
outputs_collector (BaseApplication attribute)
OutputsCollector (class in niftynet.engine.application_variables)
P
PadLayer (class in niftynet.layer.pad)
PairwiseMeasures (class in niftynet.evaluation.pairwise_measures)
PairwiseMeasuresRegression (class in niftynet.evaluation.pairwise_measures)
PairwiseResizeSampler (class in niftynet.contrib.sampler_pairwise.sampler_pairwise_resize)
(class in niftynet.contrib.sampler_pairwise.sampler_pairwise_resize_csv)
PairwiseUniformSampler (class in niftynet.contrib.sampler_pairwise.sampler_pairwise_uniform)
(class in niftynet.contrib.sampler_pairwise.sampler_pairwise_uniform_csv)
param_to_dict() (in module niftynet.io.image_reader)
ParserNamespace (class in niftynet.utilities.util_common)
patience (BaseApplication attribute)
PerComponentEvaluation (class in niftynet.evaluation.segmentation_evaluations)
PerComponentScalarEvaluation (class in niftynet.evaluation.segmentation_evaluations)
performance_history (BaseApplication attribute)
PerformanceLogger (class in niftynet.engine.handler_performance)
permutohedral_compute() (in module niftynet.layer.crf)
permutohedral_prepare() (in module niftynet.layer.crf)
phase (IterationMessage attribute)
placeholders_dict() (ImageWindow method)
plus_or_dot() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
pop_batch_op() (ImageWindowDataset method)
positive_predictive_values (class in niftynet.evaluation.segmentation_evaluations)
positive_predictive_values() (PairwiseMeasures method)
PostProcessingLayer (class in niftynet.layer.post_processing)
prelu() (in module niftynet.layer.activation)
prepare_augmentation_layers() (Preprocessing method)
prepare_normalisation_layers() (Preprocessing method)
prepare_preprocessors() (ImageReader method)
Preprocessing (class in niftynet.contrib.preprocessors.preprocessing)
print_console_vars() (ConsoleLogger method)
print_progress_bar() (in module niftynet.utilities.util_common)
print_save_input_parameters() (in module niftynet.utilities.util_common)
progress_bar_wrapper() (in module niftynet.utilities.download)
psi (GridWarperLayer attribute)
Q
quantile_25() (RegionProperties method)
quantile_75() (RegionProperties method)
R
r2() (PairwiseMeasuresRegression method)
rand_choice_coordinates() (in module niftynet.contrib.segmentation_selective_sampler.sampler_selective)
rand_init_model() (ModelRestorer method)
rand_spatial_coordinates() (in module niftynet.contrib.csv_reader.sampler_csvpatch)
(in module niftynet.contrib.csv_reader.sampler_uniform_v2_csv)
(in module niftynet.engine.sampler_uniform_v2)
RandomBiasFieldLayer (class in niftynet.layer.rand_bias_field)
RandomElasticDeformationLayer (class in niftynet.layer.rand_elastic_deform)
RandomFlipLayer (class in niftynet.layer.rand_flip)
randomise() (RandomBiasFieldLayer method)
(RandomElasticDeformationLayer method)
(RandomFlipLayer method)
(RandomRotationLayer method)
(RandomSpatialScalingLayer method)
(RandomisedLayer method)
RandomisedLayer (class in niftynet.layer.base_layer)
randomly_split_dataset() (ImageSetsPartitioner method)
RandomRotationLayer (class in niftynet.layer.rand_rotation)
RandomSpatialScalingLayer (class in niftynet.layer.rand_spatial_scaling)
RandomVectorSampler (class in niftynet.contrib.csv_reader.sampler_random_vector_v2_csv)
(class in niftynet.engine.sampler_random_vector_v2)
ratios (ImageSetsPartitioner attribute)
raw_file_url() (in module niftynet.utilities.download)
read_console_vars() (ConsoleLogger method)
read_mapping_file() (in module niftynet.utilities.histogram_standardisation)
read_tensorboard_op() (TensorBoardLogger method)
readers (BaseApplication attribute)
rectify_header_sform_qform() (in module niftynet.io.misc_io)
RegApp (class in niftynet.application.label_driven_registration)
(class in niftynet.contrib.csv_reader.applications_maybe.label_driven_registration)
RegionProperties (class in niftynet.evaluation.region_properties)
register_image_loader() (in module niftynet.io.image_loader)
register_vcs_handler() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
RegressionApplication (class in niftynet.application.regression_application)
(class in niftynet.contrib.csv_reader.applications_maybe.regression_application)
RegressionEvaluator (class in niftynet.evaluation.regression_evaluator)
RegressionRecApplication (class in niftynet.contrib.deep_boosted_regression.regression_rec_application)
regularizer_loss() (TrainableLayer method)
regularizers (TrainableLayer attribute)
RemoteConfigStore (class in niftynet.utilities.download)
RemoteProxy (class in niftynet.utilities.download)
remove_duplicated_names() (in module niftynet.utilities.util_csv)
rename_checkpoint_to_partial() (in module niftynet.contrib.checkpoint_tools.rename_checkpoint_to_partial)
render() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
render_git_describe() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
render_git_describe_long() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
render_pep440() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
render_pep440_old() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
render_pep440_post() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
render_pep440_pre() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
require_module() (in module niftynet.utilities.util_import)
REQUIRED_CONFIG_SECTION (AutoencoderApplication attribute)
,
[1]
(BaseApplication attribute)
(ClassificationApplication attribute)
,
[1]
(DecayLearningRateApplication attribute)
(GANApplication attribute)
,
[1]
(MultiClassifSegApplication attribute)
(MultiOutputApplication attribute)
(RegApp attribute)
,
[1]
(RegressionApplication attribute)
,
[1]
(RegressionRecApplication attribute)
(SegmentationApplication attribute)
,
[1]
(SegmentationApplicationBFAug attribute)
(SegmentationApplicationPatchSampler attribute)
(SelectiveSampling attribute)
ResampledFieldGridWarperLayer (class in niftynet.layer.spatial_transformer)
ResamplerLayer (class in niftynet.layer.resampler)
RescaledFieldImageGridWarperLayer (class in niftynet.layer.spatial_transformer)
reset() (ImageSetsPartitioner method)
ResidualUnit (class in niftynet.layer.residual_unit)
ResidualUpsampleLayer (class in niftynet.layer.additive_upsample)
ResizeSampler (class in niftynet.engine.sampler_resize_v2)
ResizeSamplerCSV (class in niftynet.contrib.csv_reader.sampler_resize_v2_csv)
ResizeSamplesAggregator (class in niftynet.engine.windows_aggregator_resize)
ResNet (class in niftynet.network.resnet)
ResNetDesc (class in niftynet.network.resnet)
resolve_checkpoint() (in module niftynet.io.misc_io)
resolve_file_name() (in module niftynet.io.misc_io)
resolve_module_dir() (in module niftynet.io.misc_io)
restore_from_checkpoint() (TrainableLayer method)
restore_initializer (in module niftynet.utilities.restore_initializer)
restore_model() (ModelRestorer method)
RGBHistogramEquilisationLayer (class in niftynet.layer.rgb_histogram_equilisation)
rmse (class in niftynet.evaluation.regression_evaluations)
rmse() (PairwiseMeasuresRegression method)
rmse_consistency() (in module niftynet.layer.loss_classification_multi)
rmse_loss() (in module niftynet.layer.loss_regression)
RMSProp (class in niftynet.engine.application_optimiser)
roc (class in niftynet.contrib.evaluation.classification_evaluations)
roc_auc (class in niftynet.contrib.evaluation.classification_evaluations)
run() (ApplicationDriver method)
(EvaluationApplicationDriver method)
(in module niftynet.utilities.user_parameters_parser)
run_command() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
run_threads() (ImageWindowDataset method)
(PairwiseResizeSampler method)
,
[1]
(PairwiseUniformSampler method)
,
[1]
S
sampler (BaseApplication attribute)
SamplerThreading (class in niftynet.engine.handler_sampler)
sav() (RegionProperties method)
save_csv_array() (in module niftynet.io.misc_io)
save_data_array() (in module niftynet.io.misc_io)
save_model() (ModelSaver method)
save_model_interval() (ModelSaver method)
save_volume_5d() (in module niftynet.io.misc_io)
scalar_wrapper_() (ScalarAggregator method)
ScalarAggregator (class in niftynet.evaluation.base_evaluator)
scale_2d() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
scale_3d() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
ScaleBlock (class in niftynet.network.scalenet)
ScaleNet (class in niftynet.network.scalenet)
scan_setup_py() (in module versioneer)
ScoreLayer (class in niftynet.network.holistic_net)
SE_ResNet (class in niftynet.network.se_resnet)
SE_ResNetDesc (class in niftynet.network.se_resnet)
SegmentationApplication (class in niftynet.application.segmentation_application)
(class in niftynet.contrib.csv_reader.applications_maybe.segmentation_application)
SegmentationApplicationBFAug (class in niftynet.contrib.segmentation_bf_aug.segmentation_application_bfaug)
SegmentationApplicationPatchSampler (class in niftynet.contrib.csv_reader.segmentation_application_patchsampler)
SegmentationEvaluator (class in niftynet.evaluation.segmentation_evaluator)
select_module() (in module niftynet.engine.application_factory)
selective_spatial_coordinates() (SelectiveSampler method)
SelectiveSampler (class in niftynet.contrib.segmentation_selective_sampler.sampler_selective)
SelectiveSamplerTest (class in niftynet.contrib.segmentation_selective_sampler.test_sampler_selective)
SelectiveSampling (class in niftynet.contrib.segmentation_selective_sampler.ss_app)
selu() (in module niftynet.layer.activation)
sensitivity (class in niftynet.evaluation.segmentation_evaluations)
sensitivity() (PairwiseMeasures method)
sensitivity_specificity_loss() (in module niftynet.layer.loss_segmentation)
SESS_FINISHED (in module niftynet.engine.signal)
SESS_STARTED (in module niftynet.engine.signal)
set_cuda_device() (in module niftynet.utilities.util_common)
set_iteration_update() (BaseApplication method)
(DecayLearningRateApplication method)
set_logger() (in module niftynet.io.misc_io)
set_num_threads() (ImageWindowDataset method)
set_spatial_shape() (ImageWindow method)
set_tensors_to_run() (OutputInterpreter method)
setup() (NiftyNetGlobalConfig method)
shape (SpatialImage2D attribute)
(SpatialImage3D attribute)
shapes (CSVReader attribute)
(ImageReader attribute)
(ImageWindow attribute)
(ImageWindowDataset attribute)
shear_2d() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
should_stop (IterationMessage attribute)
SimpleGAN (class in niftynet.network.simple_gan)
SimulatorGAN (class in niftynet.contrib.ultrasound_simulator_gan.ultrasound_simulator_gan)
(class in niftynet.network.simulator_gan)
singleton() (in module niftynet.utilities.decorators)
SingletonApplication (class in niftynet.application.base_application)
skewness_() (RegionProperties method)
smooth_l1_loss() (in module niftynet.layer.loss_regression)
smooth_threshold() (in module niftynet.utilities.histogram_standardisation)
SmoothingLayer (class in niftynet.layer.approximated_smoothing)
source_shape (GridWarperLayer attribute)
spatial_atleast3d() (in module niftynet.utilities.user_parameters_helper)
spatial_rank (SpatialImage2D attribute)
(SpatialImage4D attribute)
spatial_ranks (ImageReader attribute)
SpatialGradientLayer (class in niftynet.layer.spatial_gradient)
SpatialImage2D (class in niftynet.io.image_type)
SpatialImage3D (class in niftynet.io.image_type)
SpatialImage4D (class in niftynet.io.image_type)
SpatialImage5D (class in niftynet.io.image_type)
spatialnumarray() (in module niftynet.utilities.user_parameters_helper)
SpatialPriorBlock (class in niftynet.network.dense_vnet)
SpatialSELayer (class in niftynet.layer.squeeze_excitation)
specificity (class in niftynet.evaluation.segmentation_evaluations)
specificity() (PairwiseMeasures method)
split_filename() (in module niftynet.io.misc_io)
squeeze_spatial_temporal_dim() (in module niftynet.io.misc_io)
standardise_section_name() (in module niftynet.utilities.user_parameters_helper)
standardise_string() (in module niftynet.utilities.user_parameters_helper)
start_sampler_threads() (SamplerThreading method)
std_() (RegionProperties method)
stop() (BaseApplication static method)
stop_sampler_threads() (SamplerThreading method)
str2boolean() (in module niftynet.utilities.user_parameters_helper)
str_array() (in module niftynet.utilities.user_parameters_helper)
subanalyses() (CachedSubanalysisEvaluation method)
(PerComponentEvaluation method)
SubPixelLayer (class in niftynet.layer.subpixel)
sum_average() (RegionProperties method)
sum_entropy() (RegionProperties method)
sum_square_variance() (RegionProperties method)
sum_variance() (RegionProperties method)
SUPPORTED (ApplicationFactory attribute)
(ApplicationNetFactory attribute)
(EvaluationFactory attribute)
(EventHandlerFactory attribute)
(InitializerFactory attribute)
(IteratorFactory attribute)
(LossAutoencoderFactory attribute)
(LossClassificationFactory attribute)
(LossClassificationMultiFactory attribute)
(LossGANFactory attribute)
(LossRegressionFactory attribute)
(LossSegmentationFactory attribute)
(ModuleFactory attribute)
(OptimiserFactory attribute)
SUPPORTED_PHASES (BaseApplication attribute)
surface (RegionProperties attribute)
T
tensor (DilatedTensor attribute)
TensorBoardLogger (class in niftynet.engine.handler_tensorboard)
test_3d_init() (SelectiveSamplerTest method)
tf_config() (in module niftynet.utilities.util_common)
tf_dtypes (CSVReader attribute)
(ImageReader attribute)
(ImageWindow attribute)
(ImageWindowDataset attribute)
(ImageWindowDatasetCSV attribute)
tf_shapes (CSVReader attribute)
(ImageWindow attribute)
(ImageWindowDataset attribute)
(ImageWindowDatasetCSV attribute)
tile_nsamples() (CSVReader method)
tn (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
to_absolute_path() (in module niftynet.io.misc_io)
to_categorical() (CSVReader static method)
to_console_string() (IterationMessage method)
to_ohe() (CSVReader static method)
to_string() (ImageSetsPartitioner method)
(KeywordsMatching method)
(Layer method)
(PairwiseMeasures method)
(PairwiseMeasuresRegression method)
(RegionProperties method)
(TrainableLayer method)
to_tf_summary() (IterationMessage method)
total_loss (BaseApplication attribute)
touch_folder() (in module niftynet.io.misc_io)
ToyNet (class in niftynet.network.toynet)
ToyNetFeat (class in niftynet.contrib.csv_reader.toynet_features)
tp (class in niftynet.evaluation.segmentation_evaluations)
(PairwiseMeasures attribute)
train() (DataDependentLayer method)
(DiscreteLabelNormalisationLayer method)
(HistogramNormalisationLayer method)
train_files (ImageSetsPartitioner attribute)
trainable_variables() (TrainableLayer method)
TrainableLayer (class in niftynet.layer.base_layer)
transform_by_mapping() (in module niftynet.utilities.histogram_standardisation)
transform_centres() (CSVPatchSampler method)
translation_2d() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
translation_3d() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
traverse_nested() (in module niftynet.utilities.util_common)
trivial_kernel() (in module niftynet.layer.layer_util)
tversky() (in module niftynet.layer.loss_segmentation)
TwoLayerConv (class in niftynet.network.unet_2d)
type_str (ApplicationFactory attribute)
(ApplicationNetFactory attribute)
(EvaluationFactory attribute)
(EventHandlerFactory attribute)
(InitializerFactory attribute)
(IteratorFactory attribute)
(LossAutoencoderFactory attribute)
(LossClassificationFactory attribute)
(LossClassificationMultiFactory attribute)
(LossGANFactory attribute)
(LossRegressionFactory attribute)
(LossSegmentationFactory attribute)
(ModuleFactory attribute)
(OptimiserFactory attribute)
U
undecided_loss() (in module niftynet.layer.loss_segmentation)
UNet2D (class in niftynet.network.unet_2d)
UNet3D (class in niftynet.network.no_new_net)
(class in niftynet.network.unet)
UNetBlock (class in niftynet.network.no_new_net)
(class in niftynet.network.unet)
UniformSampler (class in niftynet.engine.sampler_uniform_v2)
UniformSamplerCSV (class in niftynet.contrib.csv_reader.sampler_uniform_v2_csv)
UniformUnitScaling (class in niftynet.engine.application_initializer)
union_of_seg_for_each_ref_cc() (in module niftynet.evaluation.segmentation_evaluations)
UpBlock (class in niftynet.layer.upsample_res_block)
update() (ParserNamespace method)
(RemoteProxy method)
update_if_required() (ConfigStore method)
update_performance_history() (PerformanceLogger method)
UpSampleLayer (class in niftynet.layer.upsample)
url_exists() (in module niftynet.utilities.download)
V
VAE (class in niftynet.network.vae)
validation_files (ImageSetsPartitioner attribute)
variability() (in module niftynet.layer.loss_classification_multi)
variables() (OutputsCollector method)
VarianceScaling (class in niftynet.engine.application_initializer)
variational_lower_bound() (in module niftynet.layer.loss_autoencoder)
versioneer (module)
VersioneerBadRootError
VersioneerConfig (class in niftynet.utilities.versioneer_version)
(class in versioneer)
versions_from_file() (in module versioneer)
versions_from_parentdir() (in module niftynet.utilities.versioneer_version)
(in module versioneer)
VNet (class in niftynet.network.vnet)
VNetBlock (class in niftynet.network.vnet)
vol_diff (class in niftynet.evaluation.segmentation_evaluations)
vol_diff() (PairwiseMeasures method)
volume (RegionProperties attribute)
volume_enforcement() (in module niftynet.layer.loss_segmentation)
volume_enforcement_fin() (in module niftynet.layer.loss_segmentation)
W
wasserstein_disagreement_map() (in module niftynet.layer.loss_segmentation)
weighted_mean_() (RegionProperties method)
weighted_spatial_coordinates() (in module niftynet.contrib.csv_reader.sampler_weighted_v2_csv)
(in module niftynet.engine.sampler_weighted_v2)
WeightedSampler (class in niftynet.engine.sampler_weighted_v2)
WeightedSamplerCSV (class in niftynet.contrib.csv_reader.sampler_weighted_v2_csv)
whitening_transformation() (in module niftynet.layer.mean_variance_normalisation)
WindowAsImageAggregator (class in niftynet.engine.windows_aggregator_identity)
write_all_mod_mapping() (in module niftynet.utilities.histogram_standardisation)
write_csv() (in module niftynet.utilities.util_csv)
write_tensorboard() (TensorBoardLogger method)
write_to_version_file() (in module versioneer)
Z
Zeros (class in niftynet.engine.application_initializer)
zoom_3d() (in module niftynet.contrib.csv_reader.sampler_resize_v2_csv)
(in module niftynet.engine.sampler_resize_v2)
Platform overview
Installation
Configuration file
Input filename matching
Patch-based analysis
Model zoo
Extending application
Signals and event handlers
Developing new networks
Finetuning networks
Contributor guide
niftynet
niftynet.application package
niftynet.contrib package
niftynet.engine package
niftynet.evaluation package
niftynet.io package
niftynet.layer package
niftynet.network package
niftynet.utilities package
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