Navigation
index
modules
|
NiftyNet documentation
»
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Z
A
accuracy() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
ActiLayer (class in niftynet.layer.activation)
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_customised_args() (in module niftynet.utilities.user_parameters_custom)
add_inference_args() (in module niftynet.utilities.user_parameters_default)
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() (niftynet.io.image_reader.ImageReader method)
add_to_collection() (niftynet.engine.application_variables.GradientsCollector method)
(niftynet.engine.application_variables.OutputsCollector method)
add_training_args() (in module niftynet.utilities.user_parameters_default)
Affine3DAugmentationLayer (class in niftynet.network.dense_vnet)
AffineGridWarperLayer (class in niftynet.layer.spatial_transformer)
AffineWarpConstraints (class in niftynet.layer.spatial_transformer)
ApplicationDriver (class in niftynet.engine.application_driver)
ApplicationFactory (class in niftynet.engine.application_factory)
ApplicationNetFactory (class in niftynet.engine.application_factory)
AutoencoderApplication (class in niftynet.application.autoencoder_application)
average_gradients() (in module niftynet.utilities.util_common)
B
BaseApplication (class in niftynet.application.base_application)
BaseDiscriminator (class in niftynet.layer.gan_blocks)
BaseGenerator (class in niftynet.layer.gan_blocks)
BaseNet (class in niftynet.network.base_net)
BinaryMaskingLayer (class in niftynet.layer.binary_masking)
BNLayer (class in niftynet.layer.bn)
border_distance (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
border_map() (niftynet.utilities.util_common.MorphologyOps method)
boundary_circular() (niftynet.layer.spatial_transformer.ResamplerLayer method)
boundary_replicate() (niftynet.layer.spatial_transformer.ResamplerLayer method)
boundary_symmetric() (niftynet.layer.spatial_transformer.ResamplerLayer method)
BSplineFieldImageGridWarperLayer (class in niftynet.layer.spatial_transformer)
C
CacheFunctionOutput (class in niftynet.utilities.util_common)
centre_of_mass() (niftynet.evaluation.region_properties.RegionProperties method)
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)
check_initialisations() (niftynet.application.base_application.BaseApplication method)
check_keywords() (in module niftynet.utilities.user_parameters_parser)
check_spatial_dims() (in module niftynet.layer.layer_util)
close_all() (niftynet.engine.image_window_buffer.InputBatchQueueRunner method)
coeff_shape (niftynet.layer.spatial_transformer.GridWarperLayer attribute)
com_dist() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
com_ref() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
com_seg() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
combine_with() (niftynet.layer.spatial_transformer.AffineWarpConstraints method)
compactness() (niftynet.evaluation.region_properties.RegionProperties method)
ConfigStore (class in niftynet.utilities.download)
ConfigStoreCache (class in niftynet.utilities.download)
connect_data_and_network() (niftynet.application.autoencoder_application.AutoencoderApplication method)
(niftynet.application.base_application.BaseApplication method)
(niftynet.application.gan_application.GANApplication method)
(niftynet.application.segmentation_application.SegmentationApplication method)
connected_elements() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
connected_errormaps (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
constraints (niftynet.layer.spatial_transformer.AffineGridWarperLayer attribute)
(niftynet.layer.spatial_transformer.AffineWarpConstraints attribute)
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() (niftynet.engine.image_window.ImageWindow method)
correct_image_if_necessary() (in module niftynet.io.misc_io)
create() (niftynet.engine.application_factory.ModuleFactory class method)
create_affine_pixdim() (in module niftynet.io.misc_io)
create_instance() (niftynet.io.image_type.ImageFactory class method)
create_mapping_from_multimod_arrayfiles() (in module niftynet.utilities.histogram_standardisation)
create_standard_range() (in module niftynet.utilities.histogram_standardisation)
CRFAsRNNLayer (class in niftynet.layer.crf)
crop_batch() (niftynet.engine.windows_aggregator_base.ImageWindowsAggregator static method)
CropLayer (class in niftynet.layer.crop)
cross_entropy() (in module niftynet.layer.loss_segmentation)
cross_entropy_function() (in module niftynet.layer.loss_gan)
D
DataDependentLayer (class in niftynet.layer.base_layer)
DataFromFile (class in niftynet.io.image_type)
decode_batch() (niftynet.engine.windows_aggregator_base.ImageWindowsAggregator method)
(niftynet.engine.windows_aggregator_grid.GridSamplesAggregator method)
(niftynet.engine.windows_aggregator_identity.WindowAsImageAggregator method)
(niftynet.engine.windows_aggregator_resize.ResizeSamplesAggregator 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_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() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
dice() (in module niftynet.layer.loss_segmentation)
dice_nosquare() (in module niftynet.layer.loss_segmentation)
dice_score() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
DilatedTensor (class in niftynet.layer.dilatedcontext)
DiscreteLabelNormalisationLayer (class in niftynet.layer.discrete_label_normalisation)
do_reorientation() (in module niftynet.io.misc_io)
do_resampling() (in module niftynet.io.misc_io)
download() (in module niftynet.utilities.download)
download_and_decompress() (in module niftynet.utilities.download)
download_file() (in module niftynet.utilities.download)
DownSampleLayer (class in niftynet.layer.downsample)
dtype (niftynet.io.image_type.DataFromFile attribute)
dummy_coordinates() (in module niftynet.engine.sampler_resize)
E
ElementwiseLayer (class in niftynet.layer.elementwise)
exists() (niftynet.utilities.download.ConfigStore method)
(niftynet.utilities.download.ConfigStoreCache method)
(niftynet.utilities.download.RemoteConfigStore method)
(niftynet.utilities.download.RemoteProxy method)
expand_spatial_params() (in module niftynet.layer.layer_util)
expand_to_5d() (in module niftynet.io.misc_io)
F
false_positive_rate() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
FCDecoder (class in niftynet.network.vae)
FCLayer (class in niftynet.layer.fully_connected)
file_path (niftynet.io.image_type.DataFromFile attribute)
finalise_output_op() (niftynet.engine.application_variables.OutputsCollector method)
find_set_of_labels() (in module niftynet.layer.discrete_label_normalisation)
float_array() (in module niftynet.utilities.user_parameters_helper)
fn (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
foreground_component() (niftynet.utilities.util_common.MorphologyOps method)
fp (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
from_data_reader_properties() (niftynet.engine.image_window.ImageWindow class method)
from_tuple() (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)
GANImageBlock (class in niftynet.layer.gan_blocks)
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_data() (niftynet.io.image_type.DataFromFile method)
(niftynet.io.image_type.Loadable method)
(niftynet.io.image_type.SpatialImage2D method)
(niftynet.io.image_type.SpatialImage3D method)
(niftynet.io.image_type.SpatialImage4D method)
(niftynet.io.image_type.SpatialImage5D method)
get_download_params() (niftynet.utilities.download.ConfigStoreCache method)
(niftynet.utilities.download.RemoteProxy method)
get_instance() (niftynet.engine.application_optimiser.Adagrad static method)
(niftynet.engine.application_optimiser.Adam static method)
(niftynet.engine.application_optimiser.GradientDescent static method)
(niftynet.engine.application_optimiser.Momentum static method)
get_latest_subfolder() (in module niftynet.io.misc_io)
get_local_cache_folder() (niftynet.utilities.download.ConfigStoreCache method)
get_local_path() (niftynet.utilities.download.ConfigStoreCache method)
(niftynet.utilities.download.RemoteProxy method)
get_niftynet_git_version() (in module niftynet.utilities.versioning)
get_niftynet_version() (in module niftynet.utilities.versioning)
get_niftynet_version_string() (in module niftynet.utilities.versioning)
get_sampler() (niftynet.application.base_application.BaseApplication method)
get_subject_id() (niftynet.io.image_reader.ImageReader method)
get_url() (niftynet.utilities.download.RemoteConfigStore method)
global_vars_init_or_restore() (in module niftynet.engine.application_variables)
gradient_op (niftynet.application.base_application.BaseApplication attribute)
GradientDescent (class in niftynet.engine.application_optimiser)
gradients (niftynet.engine.application_variables.GradientsCollector attribute)
GradientsCollector (class in niftynet.engine.application_variables)
gradientStub() (in module niftynet.layer.crf)
grid_spatial_coordinates() (in module niftynet.engine.sampler_grid)
GridSampler (class in niftynet.engine.sampler_grid)
GridSamplesAggregator (class in niftynet.engine.windows_aggregator_grid)
GridWarperLayer (class in niftynet.layer.spatial_transformer)
H
has_bad_inputs() (in module niftynet.utilities.util_common)
has_section_in_config() (in module niftynet.utilities.user_parameters_helper)
header_str() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
(niftynet.evaluation.pairwise_measures.PairwiseMeasuresRegression method)
(niftynet.evaluation.region_properties.RegionProperties method)
HighRes3DNet (class in niftynet.network.highres3dnet)
HighRes3DNetLarge (class in niftynet.network.highres3dnet_large)
HighRes3DNetSmall (class in niftynet.network.highres3dnet_small)
HighResBlock (class in niftynet.network.highres3dnet)
HistogramNormalisationLayer (class in niftynet.layer.histogram_normalisation)
HolisticNet (class in niftynet.network.holistic_net)
(class in niftynet.network.holistic_scalenet)
huber_loss() (in module niftynet.layer.loss_segmentation)
I
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() (niftynet.engine.image_window.ImageWindow method)
image_id (niftynet.engine.windows_aggregator_base.ImageWindowsAggregator attribute)
image_resize() (in module niftynet.network.dense_vnet)
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)
ImageWindow (class in niftynet.engine.image_window)
ImageWindowsAggregator (class in niftynet.engine.windows_aggregator_base)
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)
informedness() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
initialise_application() (niftynet.engine.application_driver.ApplicationDriver method)
initialise_dataset_loader() (niftynet.application.autoencoder_application.AutoencoderApplication method)
(niftynet.application.base_application.BaseApplication method)
(niftynet.application.gan_application.GANApplication method)
(niftynet.application.segmentation_application.SegmentationApplication method)
initialise_grid_aggregator() (niftynet.application.segmentation_application.SegmentationApplication method)
initialise_grid_sampler() (niftynet.application.segmentation_application.SegmentationApplication method)
initialise_network() (niftynet.application.autoencoder_application.AutoencoderApplication method)
(niftynet.application.base_application.BaseApplication method)
(niftynet.application.gan_application.GANApplication method)
(niftynet.application.segmentation_application.SegmentationApplication method)
initialise_reader() (niftynet.io.image_reader.ImageReader method)
initialise_resize_aggregator() (niftynet.application.segmentation_application.SegmentationApplication method)
initialise_resize_sampler() (niftynet.application.segmentation_application.SegmentationApplication method)
initialise_sampler() (niftynet.application.autoencoder_application.AutoencoderApplication method)
(niftynet.application.base_application.BaseApplication method)
(niftynet.application.gan_application.GANApplication method)
(niftynet.application.segmentation_application.SegmentationApplication method)
initialise_uniform_sampler() (niftynet.application.segmentation_application.SegmentationApplication method)
initializers (niftynet.layer.base_layer.TrainableLayer attribute)
input_image (niftynet.engine.windows_aggregator_base.ImageWindowsAggregator attribute)
input_sources (niftynet.io.image_reader.ImageReader attribute)
InputBatchQueueRunner (class in niftynet.engine.image_window_buffer)
INSTANCE_DICT (niftynet.io.image_type.ImageFactory attribute)
int_array() (in module niftynet.utilities.user_parameters_helper)
interp_order (niftynet.io.image_type.SpatialImage2D attribute)
interpret_output() (niftynet.application.autoencoder_application.AutoencoderApplication method)
(niftynet.application.base_application.BaseApplication method)
(niftynet.application.gan_application.GANApplication method)
(niftynet.application.segmentation_application.SegmentationApplication method)
intersection_over_union() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
inverse() (niftynet.layer.spatial_transformer.AffineGridWarperLayer method)
(niftynet.network.dense_vnet.Affine3DAugmentationLayer method)
inverse_op() (niftynet.layer.base_layer.Invertible method)
(niftynet.layer.discrete_label_normalisation.DiscreteLabelNormalisationLayer method)
(niftynet.layer.pad.PadLayer method)
inverse_transform() (niftynet.network.dense_vnet.Affine3DAugmentationLayer method)
Invertible (class in niftynet.layer.base_layer)
is_ready() (niftynet.layer.base_layer.DataDependentLayer method)
(niftynet.layer.discrete_label_normalisation.DiscreteLabelNormalisationLayer method)
(niftynet.layer.histogram_normalisation.HistogramNormalisationLayer method)
is_training (niftynet.application.base_application.BaseApplication attribute)
J
jaccard() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
join_subject_id_and_filename_list() (in module niftynet.utilities.util_csv)
K
key (niftynet.layer.discrete_label_normalisation.DiscreteLabelNormalisationLayer attribute)
KeywordsMatching (class in niftynet.utilities.filename_matching)
kurtosis_() (niftynet.evaluation.region_properties.RegionProperties method)
L
l1_loss() (in module niftynet.layer.loss_segmentation)
l2_loss() (in module niftynet.layer.loss_segmentation)
l2_reg_loss() (in module niftynet.layer.loss_segmentation)
Layer (class in niftynet.layer.base_layer)
layer_op() (niftynet.contrib.ultrasound_simulator_gan.ultrasound_simulator_gan.ImageDiscriminator method)
(niftynet.contrib.ultrasound_simulator_gan.ultrasound_simulator_gan.ImageGenerator method)
(niftynet.engine.sampler_grid.GridSampler method)
(niftynet.engine.sampler_linear_interpolate.LinearInterpolateSampler method)
(niftynet.engine.sampler_random_vector.RandomVectorSampler method)
(niftynet.engine.sampler_resize.ResizeSampler method)
(niftynet.engine.sampler_uniform.UniformSampler method)
(niftynet.io.image_reader.ImageReader method)
(niftynet.layer.activation.ActiLayer method)
(niftynet.layer.base_layer.Layer method)
(niftynet.layer.base_layer.LayerFromCallable method)
(niftynet.layer.binary_masking.BinaryMaskingLayer method)
(niftynet.layer.bn.BNLayer method)
(niftynet.layer.channel_sparse_convolution.ChannelSparseBNLayer method)
(niftynet.layer.channel_sparse_convolution.ChannelSparseConvLayer method)
(niftynet.layer.channel_sparse_convolution.ChannelSparseConvolutionalLayer method)
(niftynet.layer.channel_sparse_convolution.ChannelSparseDeconvLayer method)
(niftynet.layer.convolution.ConvLayer method)
(niftynet.layer.convolution.ConvolutionalLayer method)
(niftynet.layer.crf.CRFAsRNNLayer method)
(niftynet.layer.crop.CropLayer method)
(niftynet.layer.deconvolution.DeconvLayer method)
(niftynet.layer.deconvolution.DeconvolutionalLayer method)
(niftynet.layer.discrete_label_normalisation.DiscreteLabelNormalisationLayer method)
(niftynet.layer.downsample.DownSampleLayer method)
(niftynet.layer.elementwise.ElementwiseLayer method)
(niftynet.layer.fully_connected.FCLayer method)
(niftynet.layer.fully_connected.FullyConnectedLayer method)
(niftynet.layer.gan_blocks.GANImageBlock method)
(niftynet.layer.histogram_normalisation.HistogramNormalisationLayer method)
(niftynet.layer.loss_autoencoder.LossFunction method)
(niftynet.layer.loss_gan.LossFunction method)
(niftynet.layer.loss_segmentation.LossFunction method)
(niftynet.layer.mean_variance_normalisation.MeanVarNormalisationLayer method)
(niftynet.layer.pad.PadLayer method)
(niftynet.layer.post_processing.PostProcessingLayer method)
(niftynet.layer.rand_flip.RandomFlipLayer method)
(niftynet.layer.rand_rotation.RandomRotationLayer method)
(niftynet.layer.rand_spatial_scaling.RandomSpatialScalingLayer method)
(niftynet.layer.reshape.ReshapeLayer method)
(niftynet.layer.spatial_transformer.AffineGridWarperLayer method)
(niftynet.layer.spatial_transformer.BSplineFieldImageGridWarperLayer method)
(niftynet.layer.spatial_transformer.ResampledFieldGridWarperLayer method)
(niftynet.layer.spatial_transformer.ResamplerLayer method)
(niftynet.layer.spatial_transformer.RescaledFieldImageGridWarperLayer method)
(niftynet.layer.upsample.UpSampleLayer method)
(niftynet.network.deepmedic.DeepMedic method)
(niftynet.network.dense_vnet.Affine3DAugmentationLayer method)
(niftynet.network.dense_vnet.DenseFeatureStackBlock method)
(niftynet.network.dense_vnet.DenseFeatureStackBlockWithSkipAndDownsample method)
(niftynet.network.dense_vnet.DenseVNet method)
(niftynet.network.dense_vnet.SpatialPriorBlock method)
(niftynet.network.highres3dnet.HighRes3DNet method)
(niftynet.network.highres3dnet.HighResBlock method)
(niftynet.network.highres3dnet_large.HighRes3DNetLarge method)
(niftynet.network.highres3dnet_small.HighRes3DNetSmall method)
(niftynet.network.holistic_net.HolisticNet method)
(niftynet.network.holistic_net.MergeLayer method)
(niftynet.network.holistic_net.ScoreLayer method)
(niftynet.network.holistic_scalenet.HolisticNet method)
(niftynet.network.holistic_scalenet.MergeLayer method)
(niftynet.network.holistic_scalenet.ScoreLayer method)
(niftynet.network.scalenet.ScaleBlock method)
(niftynet.network.scalenet.ScaleNet method)
(niftynet.network.simple_gan.GenericGAN method)
(niftynet.network.simple_gan.ImageDiscriminator method)
(niftynet.network.simple_gan.ImageGenerator method)
(niftynet.network.simulator_gan.ImageDiscriminator method)
(niftynet.network.simulator_gan.ImageGenerator method)
(niftynet.network.toynet.ToyNet method)
(niftynet.network.unet.UNet3D method)
(niftynet.network.unet.UNetBlock method)
(niftynet.network.vae.ConvDecoder method)
(niftynet.network.vae.ConvEncoder method)
(niftynet.network.vae.FCDecoder method)
(niftynet.network.vae.GaussianSampler method)
(niftynet.network.vae.VAE method)
(niftynet.network.vnet.VNet method)
(niftynet.network.vnet.VNetBlock method)
layer_scope() (niftynet.layer.base_layer.Layer method)
LayerFromCallable (class in niftynet.layer.base_layer)
leakyRelu() (in module niftynet.layer.activation)
LinearInterpolateSampler (class in niftynet.engine.sampler_linear_interpolate)
list_depth_count() (in module niftynet.utilities.util_common)
list_labels() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
load_and_merge_csv_files() (in module niftynet.utilities.util_csv)
load_image() (in module niftynet.io.misc_io)
Loadable (class in niftynet.io.image_type)
look_up_operations() (in module niftynet.utilities.util_common)
LossAutoencoderFactory (class in niftynet.engine.application_factory)
LossFunction (class in niftynet.layer.loss_autoencoder)
(class in niftynet.layer.loss_gan)
(class in niftynet.layer.loss_segmentation)
LossGANFactory (class in niftynet.engine.application_factory)
LossSegmentationFactory (class in niftynet.engine.application_factory)
M
mae() (niftynet.evaluation.pairwise_measures.PairwiseMeasuresRegression method)
main() (in module niftynet)
(in module niftynet.contrib.checkpoint_tools.rename_checkpoint_to_partial)
(in module niftynet.utilities.download)
make_affine() (in module niftynet.io.simple_itk_as_nibabel)
make_callable_loss_func() (niftynet.layer.loss_autoencoder.LossFunction method)
(niftynet.layer.loss_gan.LossFunction method)
(niftynet.layer.loss_segmentation.LossFunction method)
make_input_tuple() (in module niftynet.utilities.user_parameters_helper)
markedness() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
mask (niftynet.layer.spatial_transformer.AffineWarpConstraints attribute)
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() (niftynet.engine.image_window.ImageWindow method)
match_ndim() (in module niftynet.layer.pad)
match_second_degree() (in module niftynet.utilities.util_csv)
matching_subjects_and_filenames() (niftynet.utilities.filename_matching.KeywordsMatching method)
max_() (niftynet.evaluation.region_properties.RegionProperties method)
mean_() (niftynet.evaluation.region_properties.RegionProperties method)
MeanVarNormalisationLayer (class in niftynet.layer.mean_variance_normalisation)
measured_average_distance() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
measured_distance() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
measured_hausdorff_distance() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
median_() (niftynet.evaluation.region_properties.RegionProperties method)
MergeLayer (class in niftynet.network.holistic_net)
(class in niftynet.network.holistic_scalenet)
min_() (niftynet.evaluation.region_properties.RegionProperties method)
ModuleFactory (class in niftynet.engine.application_factory)
Momentum (class in niftynet.engine.application_optimiser)
MorphologyOps (class in niftynet.utilities.util_common)
mse() (niftynet.evaluation.pairwise_measures.PairwiseMeasuresRegression method)
N
n_intersection (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
n_neg_ref (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
n_neg_seg (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
n_pos_ref (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
n_pos_seg (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
n_union (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
name (niftynet.io.image_type.DataFromFile attribute)
names (niftynet.io.image_reader.ImageReader attribute)
negative_predictive_values() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
net (niftynet.application.base_application.BaseApplication attribute)
niftynet (module)
,
[1]
niftynet.application (module)
,
[1]
niftynet.application.autoencoder_application (module)
niftynet.application.base_application (module)
niftynet.application.gan_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.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_optimiser (module)
niftynet.engine.application_variables (module)
niftynet.engine.image_window (module)
niftynet.engine.image_window_buffer (module)
niftynet.engine.sampler_grid (module)
niftynet.engine.sampler_linear_interpolate (module)
niftynet.engine.sampler_random_vector (module)
niftynet.engine.sampler_resize (module)
niftynet.engine.sampler_uniform (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.pairwise_measures (module)
niftynet.evaluation.region_properties (module)
niftynet.io (module)
,
[1]
niftynet.io.image_reader (module)
niftynet.io.image_type (module)
niftynet.io.misc_io (module)
niftynet.io.simple_itk_as_nibabel (module)
niftynet.layer (module)
,
[1]
niftynet.layer.activation (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.elementwise (module)
niftynet.layer.fully_connected (module)
niftynet.layer.gan_blocks (module)
niftynet.layer.histogram_normalisation (module)
niftynet.layer.layer_util (module)
niftynet.layer.loss_autoencoder (module)
niftynet.layer.loss_gan (module)
niftynet.layer.loss_segmentation (module)
niftynet.layer.mean_variance_normalisation (module)
niftynet.layer.pad (module)
niftynet.layer.post_processing (module)
niftynet.layer.rand_flip (module)
niftynet.layer.rand_rotation (module)
niftynet.layer.rand_spatial_scaling (module)
niftynet.layer.reshape (module)
niftynet.layer.spatial_transformer (module)
niftynet.layer.upsample (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.holistic_scalenet (module)
niftynet.network.scalenet (module)
niftynet.network.simple_gan (module)
niftynet.network.simulator_gan (module)
niftynet.network.toynet (module)
niftynet.network.unet (module)
niftynet.network.vae (module)
niftynet.network.vnet (module)
niftynet.utilities (module)
,
[1]
niftynet.utilities.download (module)
niftynet.utilities.filename_matching (module)
niftynet.utilities.histogram_standardisation (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.versioning (module)
no_constraints() (niftynet.layer.spatial_transformer.AffineWarpConstraints class method)
no_shear_2d() (niftynet.layer.spatial_transformer.AffineWarpConstraints class method)
no_shear_3d() (niftynet.layer.spatial_transformer.AffineWarpConstraints class method)
num_dim (niftynet.layer.spatial_transformer.AffineWarpConstraints attribute)
num_free_params (niftynet.layer.spatial_transformer.AffineWarpConstraints attribute)
num_output_channels() (niftynet.layer.post_processing.PostProcessingLayer method)
num_trainable_params() (niftynet.layer.base_layer.TrainableLayer method)
O
optimiser (niftynet.application.base_application.BaseApplication attribute)
OptimiserFactory (class in niftynet.engine.application_factory)
original_affine (niftynet.io.image_type.SpatialImage2D attribute)
original_axcodes (niftynet.io.image_type.SpatialImage2D attribute)
original_pixdim (niftynet.io.image_type.SpatialImage2D attribute)
otsu_threshold() (in module niftynet.utilities.util_common)
outline_error() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
output_axcodes (niftynet.io.image_type.SpatialImage2D attribute)
(niftynet.io.image_type.SpatialImage3D attribute)
output_decoder (niftynet.application.base_application.BaseApplication attribute)
output_pixdim (niftynet.io.image_type.SpatialImage2D attribute)
(niftynet.io.image_type.SpatialImage3D attribute)
output_shape (niftynet.layer.spatial_transformer.GridWarperLayer 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)
permutohedral_compute() (in module niftynet.layer.crf)
permutohedral_gen() (in module niftynet.layer.crf)
permutohedral_prepare() (in module niftynet.layer.crf)
placeholders_dict() (niftynet.engine.image_window.ImageWindow method)
pop_batch_op() (niftynet.engine.image_window_buffer.InputBatchQueueRunner method)
positive_predictive_values() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
PostProcessingLayer (class in niftynet.layer.post_processing)
prelu() (in module niftynet.layer.activation)
prepare_preprocessors() (niftynet.io.image_reader.ImageReader method)
print_progress_bar() (in module niftynet.utilities.util_common)
print_save_input_parameters() (in module niftynet.utilities.util_common)
psi (niftynet.layer.spatial_transformer.GridWarperLayer attribute)
py_func() (in module niftynet.layer.crf)
Q
quantile_25() (niftynet.evaluation.region_properties.RegionProperties method)
quantile_75() (niftynet.evaluation.region_properties.RegionProperties method)
R
r2() (niftynet.evaluation.pairwise_measures.PairwiseMeasuresRegression method)
rand_spatial_coordinates() (in module niftynet.engine.sampler_uniform)
random_transform() (niftynet.network.dense_vnet.Affine3DAugmentationLayer method)
RandomFlipLayer (class in niftynet.layer.rand_flip)
randomise() (niftynet.layer.base_layer.RandomisedLayer method)
(niftynet.layer.rand_flip.RandomFlipLayer method)
(niftynet.layer.rand_rotation.RandomRotationLayer method)
(niftynet.layer.rand_spatial_scaling.RandomSpatialScalingLayer method)
RandomisedLayer (class in niftynet.layer.base_layer)
RandomRotationLayer (class in niftynet.layer.rand_rotation)
RandomSpatialScalingLayer (class in niftynet.layer.rand_spatial_scaling)
RandomVectorSampler (class in niftynet.engine.sampler_random_vector)
read_mapping_file() (in module niftynet.utilities.histogram_standardisation)
reader (niftynet.application.base_application.BaseApplication attribute)
rectify_header_sform_qform() (in module niftynet.io.misc_io)
RegionProperties (class in niftynet.evaluation.region_properties)
regularizer_loss() (niftynet.layer.base_layer.TrainableLayer method)
regularizers (niftynet.layer.base_layer.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)
REQUIRED_CONFIG_SECTION (niftynet.application.autoencoder_application.AutoencoderApplication attribute)
(niftynet.application.base_application.BaseApplication attribute)
(niftynet.application.gan_application.GANApplication attribute)
(niftynet.application.segmentation_application.SegmentationApplication attribute)
resample_bspline() (niftynet.layer.spatial_transformer.ResamplerLayer method)
resample_linear() (niftynet.layer.spatial_transformer.ResamplerLayer method)
resample_nearest() (niftynet.layer.spatial_transformer.ResamplerLayer method)
ResampledFieldGridWarperLayer (class in niftynet.layer.spatial_transformer)
ResamplerLayer (class in niftynet.layer.spatial_transformer)
RescaledFieldImageGridWarperLayer (class in niftynet.layer.spatial_transformer)
ReshapeLayer (class in niftynet.layer.reshape)
ResizeSampler (class in niftynet.engine.sampler_resize)
ResizeSamplesAggregator (class in niftynet.engine.windows_aggregator_resize)
resolve_checkpoint() (in module niftynet.io.misc_io)
restore_from_checkpoint() (niftynet.layer.base_layer.TrainableLayer method)
restore_initializer (in module niftynet.utilities.restore_initializer)
rmse() (niftynet.evaluation.pairwise_measures.PairwiseMeasuresRegression method)
run() (in module niftynet.utilities.user_parameters_parser)
run_application() (niftynet.engine.application_driver.ApplicationDriver method)
run_threads() (niftynet.engine.image_window_buffer.InputBatchQueueRunner method)
S
sampler (niftynet.application.base_application.BaseApplication attribute)
sav() (niftynet.evaluation.region_properties.RegionProperties method)
save_data_array() (in module niftynet.io.misc_io)
save_volume_5d() (in module niftynet.io.misc_io)
scale_2d() (niftynet.layer.spatial_transformer.AffineWarpConstraints class method)
scale_3d() (niftynet.layer.spatial_transformer.AffineWarpConstraints class method)
ScaleBlock (class in niftynet.network.scalenet)
ScaleNet (class in niftynet.network.scalenet)
ScoreLayer (class in niftynet.network.holistic_net)
(class in niftynet.network.holistic_scalenet)
SegmentationApplication (class in niftynet.application.segmentation_application)
select_module() (in module niftynet.engine.application_factory)
selu() (in module niftynet.layer.activation)
sensitivity() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
sensitivity_specificity_loss() (in module niftynet.layer.loss_segmentation)
set_cuda_device() (in module niftynet.utilities.util_common)
set_logger() (in module niftynet.io.misc_io)
set_network_update_op() (niftynet.application.base_application.BaseApplication method)
set_spatial_shape() (niftynet.engine.image_window.ImageWindow method)
shape (niftynet.io.image_type.SpatialImage2D attribute)
(niftynet.io.image_type.SpatialImage3D attribute)
shapes (niftynet.io.image_reader.ImageReader attribute)
shear_2d() (niftynet.layer.spatial_transformer.AffineWarpConstraints class method)
SimpleGAN (class in niftynet.network.simple_gan)
SimpleITKAsNibabel (class in niftynet.io.simple_itk_as_nibabel)
SimpleITKAsNibabelHeader (class in niftynet.io.simple_itk_as_nibabel)
SimulatorGAN (class in niftynet.contrib.ultrasound_simulator_gan.ultrasound_simulator_gan)
(class in niftynet.network.simulator_gan)
SingletonApplication (class in niftynet.application.base_application)
skewness_() (niftynet.evaluation.region_properties.RegionProperties method)
smooth_threshold() (in module niftynet.utilities.histogram_standardisation)
source_shape (niftynet.layer.spatial_transformer.GridWarperLayer attribute)
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)
specificity() (niftynet.evaluation.pairwise_measures.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)
std_() (niftynet.evaluation.region_properties.RegionProperties method)
stop() (niftynet.application.base_application.BaseApplication method)
str2boolean() (in module niftynet.utilities.user_parameters_helper)
str_array() (in module niftynet.utilities.user_parameters_helper)
SUPPORTED (niftynet.engine.application_factory.ApplicationFactory attribute)
(niftynet.engine.application_factory.ApplicationNetFactory attribute)
(niftynet.engine.application_factory.LossAutoencoderFactory attribute)
(niftynet.engine.application_factory.LossGANFactory attribute)
(niftynet.engine.application_factory.LossSegmentationFactory attribute)
(niftynet.engine.application_factory.ModuleFactory attribute)
(niftynet.engine.application_factory.OptimiserFactory attribute)
surface (niftynet.evaluation.region_properties.RegionProperties attribute)
T
tensor (niftynet.layer.dilatedcontext.DilatedTensor attribute)
tf_dtypes (niftynet.io.image_reader.ImageReader attribute)
tn (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
to_string() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
(niftynet.evaluation.pairwise_measures.PairwiseMeasuresRegression method)
(niftynet.evaluation.region_properties.RegionProperties method)
(niftynet.layer.base_layer.Layer method)
(niftynet.layer.base_layer.TrainableLayer method)
touch_folder() (in module niftynet.io.misc_io)
ToyNet (class in niftynet.network.toynet)
tp (niftynet.evaluation.pairwise_measures.PairwiseMeasures attribute)
train() (niftynet.layer.base_layer.DataDependentLayer method)
(niftynet.layer.discrete_label_normalisation.DiscreteLabelNormalisationLayer method)
(niftynet.layer.histogram_normalisation.HistogramNormalisationLayer method)
trainable_variables() (niftynet.layer.base_layer.TrainableLayer method)
TrainableLayer (class in niftynet.layer.base_layer)
training_ops() (niftynet.application.base_application.BaseApplication method)
transform_by_mapping() (in module niftynet.utilities.histogram_standardisation)
translation_2d() (niftynet.layer.spatial_transformer.AffineWarpConstraints class method)
translation_3d() (niftynet.layer.spatial_transformer.AffineWarpConstraints class method)
trivial_kernel() (in module niftynet.layer.layer_util)
type_str (niftynet.engine.application_factory.ApplicationFactory attribute)
(niftynet.engine.application_factory.ApplicationNetFactory attribute)
(niftynet.engine.application_factory.LossAutoencoderFactory attribute)
(niftynet.engine.application_factory.LossGANFactory attribute)
(niftynet.engine.application_factory.LossSegmentationFactory attribute)
(niftynet.engine.application_factory.ModuleFactory attribute)
(niftynet.engine.application_factory.OptimiserFactory attribute)
U
UNet3D (class in niftynet.network.unet)
UNetBlock (class in niftynet.network.unet)
UniformSampler (class in niftynet.engine.sampler_uniform)
update() (niftynet.utilities.download.RemoteProxy method)
update_if_required() (niftynet.utilities.download.ConfigStore method)
UpSampleLayer (class in niftynet.layer.upsample)
url_exists() (in module niftynet.utilities.download)
V
VAE (class in niftynet.network.vae)
variables() (niftynet.engine.application_variables.OutputsCollector method)
variational_lower_bound() (in module niftynet.layer.loss_autoencoder)
VNet (class in niftynet.network.vnet)
VNetBlock (class in niftynet.network.vnet)
vol_diff() (niftynet.evaluation.pairwise_measures.PairwiseMeasures method)
volume (niftynet.evaluation.region_properties.RegionProperties attribute)
W
wasserstein_disagreement_map() (in module niftynet.layer.loss_segmentation)
weighted_mean_() (niftynet.evaluation.region_properties.RegionProperties method)
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)
Z
zoom_3d() (in module niftynet.engine.sampler_resize)
Quick search
Navigation
index
modules
|
NiftyNet documentation
»