Index

A

AggNet_from_file() (in module pyMSDtorch.core.networks.AggNet) aggregate() (pyMSDtorch.core.networks.SMSNet.SMSNet method)

AggregateNet (class in pyMSDtorch.core.networks.AggNet) assign_size() (in module pyMSDtorch.core.networks.graph_utils) autoencode_and_classify_training() (in module pyMSDtorch.core.train_scripts)

B

binary_acc() (in module pyMSDtorch.core.helpers) build_data_mixed_level_sets_2d() (in module pyMSDtorch.test_data.twoD.build_test_data) build_data_standard_sets_2d() (in module pyMSDtorch.test_data.twoD.build_test_data) build_data_standard_sets_2d_time() (in module pyMSDtorch.test_data.twoD.build_test_data) build_down_operator() (in module pyMSDtorch.core.networks.TUNet) build_matrix() (pyMSDtorch.core.networks.MSD_graph_tools.RandomMultiSourceMultiSinkGraph method) build_network() (pyMSDtorch.core.networks.SMSNet.SMSNet method)

build_output_layer() (pyMSDtorch.core.networks.TUNet.TUNet method) build_random_shape_set() (in module pyMSDtorch.test_data.twoD.random_shapes) build_random_shape_set_numpy() (in module pyMSDtorch.test_data.twoD.random_shapes) build_unet_layer() (pyMSDtorch.core.networks.TUNet.TUNet method) build_up_operator() (in module pyMSDtorch.core.networks.TUNet) buildSMSdilations() (in module pyMSDtorch.core.networks.SMSNet) buildSMSnodechannels() (in module pyMSDtorch.core.networks.SMSNet)

C

cc() (in module pyMSDtorch.core.corcoef) Circle (class in pyMSDtorch.test_data.twoD.random_shapes) Conv2DReLU() (in module pyMSDtorch.core.networks.SMSNet) conv_padding() (in module pyMSDtorch.core.networks.scale_up_down)

count_conv2d() (in module pyMSDtorch.core.helpers) count_conv3d() (in module pyMSDtorch.core.helpers) count_parameters() (in module pyMSDtorch.core.helpers) create_class_mapping() (in module pyMSDtorch.core.helpers) create_mask() (in module pyMSDtorch.core.helpers)

D

DataMaker (class in pyMSDtorch.test_data.twoD.noisy_gauss_2d) (class in pyMSDtorch.test_data.twoD.noisy_gauss_2d_time) DiceBCELoss (class in pyMSDtorch.core.custom_losses) DiceLoss (class in pyMSDtorch.core.custom_losses)

diffusion_2d() (in module pyMSDtorch.test_data.twoD.diffusion_model) Donut (class in pyMSDtorch.test_data.twoD.random_shapes) draw_dilations() (pyMSDtorch.core.networks.MSD_graph_tools.RandomMultiSourceMultiSinkGraph method) draw_random_dag() (in module pyMSDtorch.core.networks.MSD_graph_tools)

E

edges_source_sink_list() (in module pyMSDtorch.core.networks.SMSNet)

F

FixedSizeDoubleConv (class in pyMSDtorch.core.networks.UNet) FocalLoss (class in pyMSDtorch.core.custom_losses) FocalTverskyLoss (class in pyMSDtorch.core.custom_losses) forward() (pyMSDtorch.core.custom_losses.DiceBCELoss method) (pyMSDtorch.core.custom_losses.DiceLoss method) (pyMSDtorch.core.custom_losses.FocalLoss method) (pyMSDtorch.core.custom_losses.FocalTverskyLoss method) (pyMSDtorch.core.custom_losses.L1LossMasked method) (pyMSDtorch.core.custom_losses.MSELossMasked method) (pyMSDtorch.core.custom_losses.TverskyLoss method) (pyMSDtorch.core.networks.AggNet.AggregateNet method) (pyMSDtorch.core.networks.MSDNet.MixedScaleDenseLayer method) (pyMSDtorch.core.networks.SMSNet.SMS_reservoir method) (pyMSDtorch.core.networks.SMSNet.SMSNet method) (pyMSDtorch.core.networks.TUNet.TUNet method) (pyMSDtorch.core.networks.UNet.FixedSizeDoubleConv method) (pyMSDtorch.core.networks.UNet.UNet method)

G

generate_data_with_normal_noise() (pyMSDtorch.test_data.twoD.noisy_gauss_2d.DataMaker method) (pyMSDtorch.test_data.twoD.noisy_gauss_2d.MixedNoiseDataMaker method) generate_data_with_uniform_noise() (pyMSDtorch.test_data.twoD.noisy_gauss_2d_time.DataMaker method) generate_ground_truth_image_stack() (pyMSDtorch.test_data.twoD.noisy_gauss_2d.DataMaker method) (pyMSDtorch.test_data.twoD.noisy_gauss_2d.MixedNoiseDataMaker method) (pyMSDtorch.test_data.twoD.noisy_gauss_2d_time.DataMaker method)

get_device() (in module pyMSDtorch.core.helpers) get_in_channels() (in module pyMSDtorch.core.helpers) get_out_channels() (in module pyMSDtorch.core.helpers) get_outpadding_convT() (in module pyMSDtorch.core.networks.scale_up_down) get_outpadding_upsampling() (in module pyMSDtorch.core.networks.scale_up_down) get_random_object() (in module pyMSDtorch.test_data.twoD.random_shapes) get_random_rotation() (pyMSDtorch.test_data.twoD.random_shapes.Shape method)

H

Hdf5Dataset2D (class in pyMSDtorch.test_data.twoD.torch_hdf5_loader) Hdf5Dataset2DClasses (class in pyMSDtorch.test_data.twoD.torch_hdf5_loader)

Hdf5Dataset2Dtime (class in pyMSDtorch.test_data.twoD.torch_hdf5_loader) hello_world() (in module pyMSDtorch.test_data.twoD.tst)

I

Identity() (in module pyMSDtorch.core.networks.SMSNet)

initialize_weights() (in module pyMSDtorch.core.networks.SMSNet)

L

L1LossMasked (class in pyMSDtorch.core.custom_losses) Linear() (in module pyMSDtorch.core.networks.SMSNet)

LinearReLU() (in module pyMSDtorch.core.networks.SMSNet) LinearSigmoid() (in module pyMSDtorch.core.networks.SMSNet)

M

make_dir() (in module pyMSDtorch.core.helpers) max_pool_size_result() (in module pyMSDtorch.core.networks.TUNet) MixedNoiseDataMaker (class in pyMSDtorch.test_data.twoD.noisy_gauss_2d) MixedScaleDenseLayer (class in pyMSDtorch.core.networks.MSDNet) MixedScaleDenseNetwork (class in pyMSDtorch.core.networks.MSDNet) module pyMSDtorch pyMSDtorch.core pyMSDtorch.core.corcoef pyMSDtorch.core.custom_losses pyMSDtorch.core.helpers pyMSDtorch.core.networks pyMSDtorch.core.networks.AggNet pyMSDtorch.core.networks.graph_utils pyMSDtorch.core.networks.MSD_graph_tools pyMSDtorch.core.networks.MSDNet pyMSDtorch.core.networks.scale_up_down pyMSDtorch.core.networks.SMSNet pyMSDtorch.core.networks.TUNet pyMSDtorch.core.networks.UNet pyMSDtorch.core.train_scripts pyMSDtorch.test_data pyMSDtorch.test_data.twoD pyMSDtorch.test_data.twoD.build_test_data pyMSDtorch.test_data.twoD.diffusion_model pyMSDtorch.test_data.twoD.noisy_gauss_2d pyMSDtorch.test_data.twoD.noisy_gauss_2d_time pyMSDtorch.test_data.twoD.random_shapes pyMSDtorch.test_data.twoD.torch_hdf5_loader pyMSDtorch.test_data.twoD.tst pyMSDtorch.viz_tools pyMSDtorch.viz_tools.plots

MSDNetwork_from_file() (in module pyMSDtorch.core.networks.MSDNet) MSELossMasked (class in pyMSDtorch.core.custom_losses)

N

network_stats() (in module pyMSDtorch.core.networks.SMSNet)

node_model() (pyMSDtorch.core.networks.graph_utils.random_graph_MT method)

P

plot_heatmap_and_labels() (in module pyMSDtorch.viz_tools.plots) plot_rgb_and_labels() (in module pyMSDtorch.viz_tools.plots) plot_shapes_data_numpy() (in module pyMSDtorch.viz_tools.plots) plot_training_results_regression() (in module pyMSDtorch.viz_tools.plots) plot_training_results_segmentation() (in module pyMSDtorch.viz_tools.plots) pyMSDtorch module pyMSDtorch.core module pyMSDtorch.core.corcoef module pyMSDtorch.core.custom_losses module pyMSDtorch.core.helpers module pyMSDtorch.core.networks module pyMSDtorch.core.networks.AggNet module pyMSDtorch.core.networks.graph_utils module pyMSDtorch.core.networks.MSD_graph_tools module pyMSDtorch.core.networks.MSDNet module pyMSDtorch.core.networks.scale_up_down module pyMSDtorch.core.networks.SMSNet module

pyMSDtorch.core.networks.TUNet module pyMSDtorch.core.networks.UNet module pyMSDtorch.core.train_scripts module pyMSDtorch.test_data module pyMSDtorch.test_data.twoD module pyMSDtorch.test_data.twoD.build_test_data module pyMSDtorch.test_data.twoD.diffusion_model module pyMSDtorch.test_data.twoD.noisy_gauss_2d module pyMSDtorch.test_data.twoD.noisy_gauss_2d_time module pyMSDtorch.test_data.twoD.random_shapes module pyMSDtorch.test_data.twoD.torch_hdf5_loader module pyMSDtorch.test_data.twoD.tst module pyMSDtorch.viz_tools module pyMSDtorch.viz_tools.plots module

R

random_circle() (in module pyMSDtorch.test_data.twoD.random_shapes) random_DAG() (in module pyMSDtorch.core.networks.MSD_graph_tools) random_DAG_scale_free() (in module pyMSDtorch.core.networks.MSD_graph_tools) random_donut() (in module pyMSDtorch.test_data.twoD.random_shapes) random_graph() (pyMSDtorch.core.networks.graph_utils.random_graph_MT method) random_graph_MT (class in pyMSDtorch.core.networks.graph_utils) random_LL_graph() (in module pyMSDtorch.core.networks.graph_utils) random_rectangle() (in module pyMSDtorch.test_data.twoD.random_shapes) random_SMS_network() (in module pyMSDtorch.core.networks.SMSNet)

random_triangle() (in module pyMSDtorch.test_data.twoD.random_shapes) RandomCrop_Dataset (class in pyMSDtorch.core.helpers) RandomMultiSourceMultiSinkGraph (class in pyMSDtorch.core.networks.MSD_graph_tools) Rectangle (class in pyMSDtorch.test_data.twoD.random_shapes) regression_metrics() (in module pyMSDtorch.core.train_scripts) reset() (pyMSDtorch.core.networks.SMSNet.SMSNet method) resulting_conv_size() (in module pyMSDtorch.core.networks.scale_up_down) resulting_convT_size() (in module pyMSDtorch.core.networks.scale_up_down) run_tst() (in module pyMSDtorch.test_data.twoD.noisy_gauss_2d) (in module pyMSDtorch.test_data.twoD.noisy_gauss_2d_time)

S

save_decoded_image2d() (in module pyMSDtorch.core.helpers) save_image_reconstructions2d() (in module pyMSDtorch.core.helpers) save_loss_images() (in module pyMSDtorch.core.helpers) save_network_parameters() (pyMSDtorch.core.networks.AggNet.AggregateNet method) (pyMSDtorch.core.networks.MSDNet.MixedScaleDenseNetwork method) (pyMSDtorch.core.networks.SMSNet.SMSNet method) (pyMSDtorch.core.networks.TUNet.TUNet method) save_training_images() (in module pyMSDtorch.core.helpers)

scaling_table() (in module pyMSDtorch.core.networks.scale_up_down) segmentation_metrics() (in module pyMSDtorch.core.train_scripts) set_snr_brackets() (pyMSDtorch.test_data.twoD.noisy_gauss_2d.MixedNoiseDataMaker method) Shape (class in pyMSDtorch.test_data.twoD.random_shapes) SMS_reservoir (class in pyMSDtorch.core.networks.SMSNet) SMSNet (class in pyMSDtorch.core.networks.SMSNet) SMSNetwork_from_file() (in module pyMSDtorch.core.networks.SMSNet) sort_and_rename() (in module pyMSDtorch.core.networks.SMSNet) sparsity() (in module pyMSDtorch.core.networks.MSD_graph_tools)

T

topology_dict() (pyMSDtorch.core.networks.MSDNet.MixedScaleDenseNetwork method) (pyMSDtorch.core.networks.SMSNet.SMSNet method) (pyMSDtorch.core.networks.TUNet.TUNet method) train_autoencoder() (in module pyMSDtorch.core.train_scripts) train_labeling() (in module pyMSDtorch.core.train_scripts) train_regression() (in module pyMSDtorch.core.train_scripts) train_segmentation() (in module pyMSDtorch.core.train_scripts) training (pyMSDtorch.core.custom_losses.DiceBCELoss attribute) (pyMSDtorch.core.custom_losses.DiceLoss attribute) (pyMSDtorch.core.custom_losses.FocalLoss attribute) (pyMSDtorch.core.custom_losses.FocalTverskyLoss attribute) (pyMSDtorch.core.custom_losses.L1LossMasked attribute) (pyMSDtorch.core.custom_losses.MSELossMasked attribute) (pyMSDtorch.core.custom_losses.TverskyLoss attribute) (pyMSDtorch.core.networks.AggNet.AggregateNet attribute) (pyMSDtorch.core.networks.MSDNet.MixedScaleDenseLayer attribute) (pyMSDtorch.core.networks.SMSNet.SMS_reservoir attribute) (pyMSDtorch.core.networks.SMSNet.SMSNet attribute) (pyMSDtorch.core.networks.TUNet.TUNet attribute) (pyMSDtorch.core.networks.UNet.FixedSizeDoubleConv attribute) (pyMSDtorch.core.networks.UNet.UNet attribute)

Triangle (class in pyMSDtorch.test_data.twoD.random_shapes) tst() (in module pyMSDtorch.core.custom_losses) (in module pyMSDtorch.core.networks.graph_utils) (in module pyMSDtorch.core.networks.MSD_graph_tools) (in module pyMSDtorch.core.networks.MSDNet) (in module pyMSDtorch.core.networks.TUNet) (in module pyMSDtorch.core.networks.UNet) (in module pyMSDtorch.core.train_scripts) (in module pyMSDtorch.test_data.twoD.diffusion_model) (in module pyMSDtorch.test_data.twoD.noisy_gauss_2d) (in module pyMSDtorch.test_data.twoD.noisy_gauss_2d_time) (in module pyMSDtorch.test_data.twoD.torch_hdf5_loader) tst_directory() (in module pyMSDtorch.core.helpers) tst_mixed() (in module pyMSDtorch.test_data.twoD.noisy_gauss_2d) TUNet (class in pyMSDtorch.core.networks.TUNet) TUNetwork_from_file() (in module pyMSDtorch.core.networks.TUNet) TverskyLoss (class in pyMSDtorch.core.custom_losses)

U

UNet (class in pyMSDtorch.core.networks.UNet)

unet_sizing_chart() (in module pyMSDtorch.core.networks.TUNet)