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NiftyNet 0.2.2 documentation
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__init__ (ImageSetsPartitioner attribute)
(IterationMessage attribute)
(NiftyNetGlobalConfig attribute)
__init__() (AffineGridWarperLayer method)
(AffineWarpConstraints method)
(BSplineFieldImageGridWarperLayer method)
(CRFAsRNNLayer method)
(GridWarperLayer method)
(HistogramNormalisationLayer method)
(RandomFlipLayer method)
(ResampledFieldGridWarperLayer method)
(RescaledFieldImageGridWarperLayer method)
A
accuracy() (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() (ImageReader method)
add_to_collection() (GradientsCollector method)
(OutputsCollector method)
add_training_args() (in module niftynet.utilities.user_parameters_default)
add_validation_flag() (BaseApplication method)
Affine3DAugmentationLayer (class in niftynet.network.dense_vnet)
AffineGridWarperLayer (class in niftynet.layer.grid_warper)
AffineWarpConstraints (class in niftynet.layer.grid_warper)
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)
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 (PairwiseMeasures attribute)
border_map() (MorphologyOps method)
BSplineFieldImageGridWarperLayer (class in niftynet.layer.spatial_transformer)
C
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)
centre_of_mass() (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_binary() (PairwiseMeasures method)
check_constraint() (in module niftynet.contrib.segmentation_selective_sampler.test_sampler_selective)
check_initialisations() (BaseApplication method)
check_keywords() (in module niftynet.utilities.user_parameters_parser)
check_module() (in module niftynet.utilities.util_import)
check_spatial_dims() (in module niftynet.layer.layer_util)
close_all() (InputBatchQueueRunner method)
coeff_shape (GridWarperLayer attribute)
com_dist() (PairwiseMeasures method)
com_ref() (PairwiseMeasures method)
com_seg() (PairwiseMeasures method)
combine_with() (AffineWarpConstraints method)
compactness() (RegionProperties method)
ConfigStore (class in niftynet.utilities.download)
ConfigStoreCache (class in niftynet.utilities.download)
connect_data_and_network() (AutoencoderApplication method)
(BaseApplication method)
(DecayLearningRateApplication method)
(GANApplication method)
(RegressionApplication method)
(SegmentationApplication method)
(SelectiveSampling method)
connected_elements() (PairwiseMeasures method)
connected_errormaps (PairwiseMeasures attribute)
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)
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)
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_label_size_map() (in module niftynet.contrib.segmentation_selective_sampler.sampler_selective)
create_mapping_from_multimod_arrayfiles() (in module niftynet.utilities.histogram_standardisation)
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)
CropLayer (class in niftynet.layer.crop)
cross_entropy() (in module niftynet.layer.loss_segmentation)
cross_entropy_function() (in module niftynet.layer.loss_gan)
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)
DataFromFile (class in niftynet.io.image_type)
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_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)
dice() (in module niftynet.layer.loss_segmentation)
dice_dense() (in module niftynet.layer.loss_segmentation)
dice_nosquare() (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_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 (DataFromFile attribute)
dummy_coordinates() (in module niftynet.engine.sampler_resize)
E
ElementwiseLayer (class in niftynet.layer.elementwise)
energy() (RegionProperties method)
entropy() (RegionProperties method)
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() (PairwiseMeasures method)
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 (PairwiseMeasures attribute)
foreground_component() (MorphologyOps method)
fp (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_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_data() (DataFromFile method)
(Loadable method)
(SpatialImage2D method)
(SpatialImage3D method)
(SpatialImage4D method)
(SpatialImage5D 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_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_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_git_version() (in module niftynet.utilities.versioning)
get_niftynet_home_folder() (NiftyNetGlobalConfig method)
get_niftynet_version() (in module niftynet.utilities.versioning)
get_niftynet_version_string() (in module niftynet.utilities.versioning)
get_sampler() (BaseApplication method)
get_subject_id() (ImageReader method)
get_url() (RemoteConfigStore method)
gitlab_raw_file_url() (in module niftynet.utilities.download)
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)
gradient_op (BaseApplication attribute)
GradientDescent (class in niftynet.engine.application_optimiser)
gradients (GradientsCollector attribute)
GradientsCollector (class in niftynet.engine.application_variables)
gradientStub() (in module niftynet.layer.crf)
grep_files_by_data_section() (ImageSetsPartitioner method)
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.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)
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)
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)
home_key (NiftyNetGlobalConfig attribute)
homogeneity() (RegionProperties method)
huber_loss() (in module niftynet.layer.loss_regression)
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() (ImageWindow method)
image_id (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)
ImageSetsPartitioner (class in niftynet.io.image_sets_partitioner)
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)
inference_files (ImageSetsPartitioner attribute)
information_measure_correlation() (RegionProperties method)
informedness() (PairwiseMeasures method)
init_non_uniform_angle() (RandomRotationLayer method)
init_uniform_angle() (RandomRotationLayer method)
initialise() (ImageReader method)
(ImageSetsPartitioner method)
initialise_application() (ApplicationDriver method)
initialise_dataset_loader() (AutoencoderApplication method)
(BaseApplication method)
(GANApplication method)
(RegressionApplication method)
(SegmentationApplication method)
(SelectiveSampling method)
initialise_grid_aggregator() (RegressionApplication method)
(SegmentationApplication method)
(SelectiveSampling method)
initialise_grid_sampler() (RegressionApplication method)
(SegmentationApplication method)
(SelectiveSampling method)
initialise_network() (AutoencoderApplication method)
(BaseApplication method)
(GANApplication method)
(RegressionApplication method)
(SegmentationApplication method)
(SelectiveSampling method)
initialise_resize_aggregator() (RegressionApplication method)
(SegmentationApplication method)
initialise_resize_sampler() (RegressionApplication method)
(SegmentationApplication method)
initialise_sampler() (AutoencoderApplication method)
(BaseApplication method)
(GANApplication method)
(RegressionApplication method)
(SegmentationApplication method)
(SelectiveSampling method)
initialise_selective_sampler() (SelectiveSampling method)
initialise_uniform_sampler() (RegressionApplication method)
(SegmentationApplication method)
initialise_weighted_sampler() (RegressionApplication method)
(SegmentationApplication method)
InitializerFactory (class in niftynet.engine.application_factory)
initializers (TrainableLayer attribute)
input_image (ImageWindowsAggregator attribute)
input_sources (ImageReader attribute)
InputBatchQueueRunner (class in niftynet.engine.image_window_buffer)
INSTANCE_DICT (ImageFactory attribute)
int_array() (in module niftynet.utilities.user_parameters_helper)
interp_order (SpatialImage2D attribute)
interpret_output() (AutoencoderApplication method)
(BaseApplication method)
(GANApplication method)
(RegressionApplication method)
(SegmentationApplication method)
(SelectiveSampling method)
intersection_over_union() (PairwiseMeasures method)
inverse() (Affine3DAugmentationLayer method)
inverse_difference_moment() (RegionProperties method)
inverse_op() (AffineGridWarperLayer method)
(DiscreteLabelNormalisationLayer method)
(Invertible method)
(PadLayer method)
inverse_transform() (Affine3DAugmentationLayer method)
Invertible (class in niftynet.layer.base_layer)
is_inference (IterationMessage attribute)
is_ready() (DataDependentLayer method)
(DiscreteLabelNormalisationLayer method)
(HistogramNormalisationLayer method)
is_training (BaseApplication attribute)
(IterationMessage attribute)
is_validation (BaseApplication attribute)
(IterationMessage attribute)
iter_duration (IterationMessage attribute)
IterationMessage (class in niftynet.engine.application_iteration)
J
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)
Layer (class in niftynet.layer.base_layer)
layer_op() (ActiLayer method)
(Affine3DAugmentationLayer method)
(AffineGridWarperLayer method)
(BNLayer method)
(BSplineFieldImageGridWarperLayer method)
(BinaryMaskingLayer method)
(CRFAsRNNLayer method)
(ChannelSparseBNLayer method)
(ChannelSparseConvLayer method)
(ChannelSparseConvolutionalLayer method)
(ChannelSparseDeconvLayer method)
(ConvDecoder method)
(ConvEncoder method)
(ConvLayer method)
(ConvolutionalLayer method)
(CropLayer method)
(DeconvLayer method)
(DeconvolutionalLayer method)
(DeepMedic method)
(DenseFeatureStackBlock method)
(DenseFeatureStackBlockWithSkipAndDownsample method)
(DenseVNet method)
(DiscreteLabelNormalisationLayer method)
(DownSampleLayer method)
(ElementwiseLayer method)
(FCDecoder method)
(FCLayer method)
(FullyConnectedLayer method)
(GANImageBlock method)
(GaussianSampler method)
(GenericGAN method)
(GridSampler method)
(GridWarperLayer method)
(HighRes3DNet method)
(HighRes3DNetLarge method)
(HighRes3DNetSmall method)
(HighResBlock method)
(HistogramNormalisationLayer method)
(HolisticNet method)
(ImageDiscriminator method)
,
[1]
,
[2]
(ImageGenerator method)
,
[1]
,
[2]
(ImageReader method)
(Layer method)
(LayerFromCallable method)
(LinearInterpolateSampler method)
(LossFunction method)
,
[1]
,
[2]
,
[3]
(MeanVarNormalisationLayer method)
(MergeLayer method)
(PadLayer method)
(PostProcessingLayer method)
(RandomElasticDeformationLayer method)
(RandomFlipLayer method)
(RandomRotationLayer method)
(RandomSpatialScalingLayer method)
(RandomVectorSampler method)
(ResampledFieldGridWarperLayer method)
(ResamplerLayer method)
(RescaledFieldImageGridWarperLayer method)
(ReshapeLayer method)
(ResizeSampler method)
(ScaleBlock method)
(ScaleNet method)
(ScoreLayer method)
(SpatialPriorBlock method)
(ToyNet method)
(UNet3D method)
(UNetBlock method)
(UniformSampler method)
(UpSampleLayer method)
(VAE method)
(VNet method)
(VNetBlock 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)
list_depth_count() (in module niftynet.utilities.util_common)
list_labels() (PairwiseMeasures method)
load_data_sections_by_subject() (ImageSetsPartitioner method)
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_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() (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() (in module niftynet.io.simple_itk_as_nibabel)
make_callable_loss_func() (LossFunction method)
,
[1]
make_input_tuple() (in module niftynet.utilities.user_parameters_helper)
markedness() (PairwiseMeasures method)
mask (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() (ImageWindow method)
match_ndim() (in module niftynet.layer.pad)
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)
min_() (RegionProperties method)
min_number_from_ratio() (Constraint method)
ModuleFactory (class in niftynet.engine.application_factory)
Momentum (class in niftynet.engine.application_optimiser)
MorphologyOps (class in niftynet.utilities.util_common)
mse() (PairwiseMeasuresRegression method)
N
n_intersection (PairwiseMeasures attribute)
n_neg_ref (PairwiseMeasures attribute)
n_neg_seg (PairwiseMeasures attribute)
n_pos_ref (PairwiseMeasures attribute)
n_pos_seg (PairwiseMeasures attribute)
n_union (PairwiseMeasures attribute)
name (DataFromFile attribute)
names (ImageReader attribute)
negative_predictive_values() (PairwiseMeasures method)
NesterovMomentum (class in niftynet.engine.application_optimiser)
net (BaseApplication attribute)
new_partition (ImageSetsPartitioner 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.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.layer (module)
niftynet.contrib.layer.rand_elastic_deform (module)
niftynet.contrib.learning_rate_schedule (module)
niftynet.contrib.learning_rate_schedule.decay_lr_application (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.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.sampler_weighted (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_sets_partitioner (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.grid_warper (module)
niftynet.layer.histogram_normalisation (module)
niftynet.layer.layer_util (module)
niftynet.layer.loss_autoencoder (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_flip (module)
niftynet.layer.rand_rotation (module)
niftynet.layer.rand_spatial_scaling (module)
niftynet.layer.resampler (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.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.decorators (module)
niftynet.utilities.download (module)
niftynet.utilities.filename_matching (module)
niftynet.utilities.histogram_standardisation (module)
niftynet.utilities.niftynet_global_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.versioning (module)
niftynet_exts (NiftyNetGlobalConfig attribute)
NiftyNetGlobalConfig (class in niftynet.utilities.niftynet_global_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)
num_dim (AffineWarpConstraints attribute)
num_free_params (AffineWarpConstraints attribute)
num_output_channels() (PostProcessingLayer method)
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)
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)
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)
ParserNamespace (class in niftynet.utilities.util_common)
permutohedral_compute() (in module niftynet.layer.crf)
permutohedral_gen() (in module niftynet.layer.crf)
permutohedral_prepare() (in module niftynet.layer.crf)
phase (IterationMessage attribute)
placeholders_dict() (ImageWindow method)
pop_batch_op() (InputBatchQueueRunner method)
positive_predictive_values() (PairwiseMeasures method)
PostProcessingLayer (class in niftynet.layer.post_processing)
prelu() (in module niftynet.layer.activation)
prepare_preprocessors() (ImageReader 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)
py_func() (in module niftynet.layer.crf)
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_spatial_coordinates() (in module niftynet.engine.sampler_uniform)
random_transform() (Affine3DAugmentationLayer method)
RandomElasticDeformationLayer (class in niftynet.contrib.layer.rand_elastic_deform)
RandomFlipLayer (class in niftynet.layer.rand_flip)
randomise() (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.engine.sampler_random_vector)
ratios (ImageSetsPartitioner attribute)
read_mapping_file() (in module niftynet.utilities.histogram_standardisation)
readers (BaseApplication attribute)
rectify_header_sform_qform() (in module niftynet.io.misc_io)
RegionProperties (class in niftynet.evaluation.region_properties)
RegressionApplication (class in niftynet.application.regression_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)
REQUIRED_CONFIG_SECTION (AutoencoderApplication attribute)
(BaseApplication attribute)
(DecayLearningRateApplication attribute)
(GANApplication attribute)
(RegressionApplication attribute)
(SegmentationApplication 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)
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)
resolve_module_dir() (in module niftynet.io.misc_io)
restore_from_checkpoint() (TrainableLayer method)
restore_initializer (in module niftynet.utilities.restore_initializer)
rmse() (PairwiseMeasuresRegression method)
rmse_loss() (in module niftynet.layer.loss_regression)
RMSProp (class in niftynet.engine.application_optimiser)
run() (in module niftynet.utilities.user_parameters_parser)
run_application() (ApplicationDriver method)
run_threads() (InputBatchQueueRunner method)
run_vars() (ApplicationDriver method)
S
sampler (BaseApplication attribute)
sav() (RegionProperties method)
save_data_array() (in module niftynet.io.misc_io)
save_volume_5d() (in module niftynet.io.misc_io)
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)
ScoreLayer (class in niftynet.network.holistic_net)
SegmentationApplication (class in niftynet.application.segmentation_application)
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() (PairwiseMeasures method)
sensitivity_specificity_loss() (in module niftynet.layer.loss_segmentation)
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_network_gradient_op() (BaseApplication method)
set_spatial_shape() (ImageWindow method)
setup() (NiftyNetGlobalConfig method)
shape (SpatialImage2D attribute)
(SpatialImage3D attribute)
shapes (ImageReader attribute)
shear_2d() (niftynet.layer.grid_warper.AffineWarpConstraints class method)
should_stop (IterationMessage attribute)
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)
singleton() (in module niftynet.utilities.decorators)
SingletonApplication (class in niftynet.application.base_application)
skewness_() (RegionProperties method)
smooth_threshold() (in module niftynet.utilities.histogram_standardisation)
source_shape (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() (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_() (RegionProperties method)
stop() (BaseApplication method)
str2boolean() (in module niftynet.utilities.user_parameters_helper)
str_array() (in module niftynet.utilities.user_parameters_helper)
sum_average() (RegionProperties method)
sum_entropy() (RegionProperties method)
sum_square_variance() (RegionProperties method)
sum_variance() (RegionProperties method)
SUPPORTED (ApplicationFactory attribute)
(ApplicationNetFactory attribute)
(InitializerFactory attribute)
(LossAutoencoderFactory attribute)
(LossGANFactory attribute)
(LossRegressionFactory attribute)
(LossSegmentationFactory attribute)
(ModuleFactory attribute)
(OptimiserFactory attribute)
surface (RegionProperties attribute)
T
tensor (DilatedTensor attribute)
test_3d_init() (SelectiveSamplerTest method)
tf_dtypes (ImageReader attribute)
tn (PairwiseMeasures attribute)
to_absolute_path() (in module niftynet.io.misc_io)
to_console_string() (IterationMessage method)
to_string() (ImageSetsPartitioner method)
(Layer method)
(PairwiseMeasures method)
(PairwiseMeasuresRegression method)
(RegionProperties method)
(TrainableLayer method)
to_tf_summary() (IterationMessage method)
touch_folder() (in module niftynet.io.misc_io)
ToyNet (class in niftynet.network.toynet)
tp (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)
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)
type_str (ApplicationFactory attribute)
(ApplicationNetFactory attribute)
(InitializerFactory attribute)
(LossAutoencoderFactory attribute)
(LossGANFactory attribute)
(LossRegressionFactory attribute)
(LossSegmentationFactory attribute)
(ModuleFactory attribute)
(OptimiserFactory attribute)
U
UNet3D (class in niftynet.network.unet)
UNetBlock (class in niftynet.network.unet)
UniformSampler (class in niftynet.engine.sampler_uniform)
UniformUnitScaling (class in niftynet.engine.application_initializer)
update() (ParserNamespace method)
(RemoteProxy method)
update_if_required() (ConfigStore 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)
variables() (OutputsCollector method)
VarianceScaling (class in niftynet.engine.application_initializer)
variational_lower_bound() (in module niftynet.layer.loss_autoencoder)
VNet (class in niftynet.network.vnet)
VNetBlock (class in niftynet.network.vnet)
vol_diff() (PairwiseMeasures method)
volume (RegionProperties attribute)
W
wasserstein_disagreement_map() (in module niftynet.layer.loss_segmentation)
weighted_mean_() (RegionProperties method)
weighted_spatial_coordinates() (in module niftynet.engine.sampler_weighted)
WeightedSampler (class in niftynet.engine.sampler_weighted)
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)
Z
Zeros (class in niftynet.engine.application_initializer)
zoom_3d() (in module niftynet.engine.sampler_resize)
Installation
Configuration file
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Developing new networks
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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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