Index

_

__getitem__() (neuro_morpho.data.data_loader.NeuroMorphoDataset method) __len__() (neuro_morpho.data.data_loader.NeuroMorphoDataset method) __project__ (in module neuro_morpho) __version__ (in module neuro_morpho) _aggregate_results() (in module neuro_morpho.reports.generator)

_channels (neuro_morpho.model.unet.Decoder attribute) (neuro_morpho.model.unet.Encoder attribute) _config_line_filter() (in module neuro_morpho.run) _config_line_to_pair() (in module neuro_morpho.run) _parse_single_file() (in module neuro_morpho.reports.generator) _single_factor (neuro_morpho.model.transforms.DownSample attribute)

A

accuracy() (in module neuro_morpho.model.metrics) alpha (neuro_morpho.model.loss.WeightedFocalLoss attribute) analyze_breaks() (neuro_morpho.model.breaks_analyzer.BreaksAnalyzer method)

apply_tpl() (in module neuro_morpho.model.unet) AttentionGroup (class in neuro_morpho.model.unet) aug_transform (neuro_morpho.data.data_loader.NeuroMorphoDataset attribute) avg_pool (neuro_morpho.model.unet.ChannelAttention attribute)

B

BaseModel (class in neuro_morpho.model.base) bn (neuro_morpho.model.unet.Conv2d attribute) (neuro_morpho.model.unet.UpConv2d attribute)

BreaksAnalyzer (class in neuro_morpho.model.breaks_analyzer) build_dataloader() (in module neuro_morpho.data.data_loader)

C

calculate_branch_lengths() (in module neuro_morpho.reports.stats) calculate_n_branches() (in module neuro_morpho.reports.stats) calculate_n_tip_points() (in module neuro_morpho.reports.stats) calculate_total_length() (in module neuro_morpho.reports.stats) cast_and_move() (in module neuro_morpho.model.unet) cast_fn (neuro_morpho.model.unet.UNet attribute) ChannelAttention (class in neuro_morpho.model.unet) class_accuracy() (in module neuro_morpho.model.metrics) coefs (neuro_morpho.model.loss.WeightedMap attribute) CombinedLoss (class in neuro_morpho.model.loss) CometLogger (class in neuro_morpho.logging.comet)

config_str_to_dict() (in module neuro_morpho.run) conv (neuro_morpho.model.unet.Conv2d attribute) (neuro_morpho.model.unet.UpConv2d attribute) conv1 (neuro_morpho.model.unet.AttentionGroup attribute) (neuro_morpho.model.unet.DoubleConv2d attribute) (neuro_morpho.model.unet.SpatialAttention attribute) conv2 (neuro_morpho.model.unet.AttentionGroup attribute) (neuro_morpho.model.unet.DoubleConv2d attribute) Conv2d (class in neuro_morpho.model.unet) conv3 (neuro_morpho.model.unet.AttentionGroup attribute) conv_1x1 (neuro_morpho.model.unet.AttentionGroup attribute) create_connecting_line() (neuro_morpho.model.breaks_analyzer.BreaksAnalyzer method)

D

Decoder (class in neuro_morpho.model.unet) decoder (neuro_morpho.model.unet.UNetModule attribute) detach_and_move() (in module neuro_morpho.model.unet)

device (neuro_morpho.model.unet.UNet attribute) distribution_comparison() (in module neuro_morpho.reports.report) DoubleConv2d (class in neuro_morpho.model.unet) DownSample (class in neuro_morpho.model.transforms)

E

Encoder (class in neuro_morpho.model.unet) encoder (neuro_morpho.model.unet.UNetModule attribute) eps (neuro_morpho.model.transforms.Norm2One attribute) (neuro_morpho.model.transforms.Standardize attribute) ERR_COLS_DONT_MATCH (in module neuro_morpho.reports.report) ERR_INVALID_DIST (in module neuro_morpho.reports.stats) ERR_MISSING_FNAME_COL (in module neuro_morpho.reports.report)

ERR_NOT_IMPLEMENTED (in module neuro_morpho.model.base) (in module neuro_morpho.reports.report) ERR_PREDICT_DIR_NOT_IMPLEMENTED (in module neuro_morpho.model.unet) exp_id (neuro_morpho.model.unet.UNet attribute) experiment (neuro_morpho.logging.comet.CometLogger attribute) extend_image_shape() (neuro_morpho.model.tiler.Tiler method) extract_branch_ids() (in module neuro_morpho.reports.stats)

F

fc (neuro_morpho.model.unet.ChannelAttention attribute) find_package_location() (in module neuro_morpho.util) find_repo_location() (in module neuro_morpho.util) find_threshold() (neuro_morpho.model.base.BaseModel method) (neuro_morpho.model.unet.UNet method) fit() (neuro_morpho.model.base.BaseModel method) (neuro_morpho.model.simple_baseline.SimpleBaseLine method) (neuro_morpho.model.unet.UNet method) forward() (neuro_morpho.model.loss.CombinedLoss method) (neuro_morpho.model.loss.SigmoidDiceLoss method) (neuro_morpho.model.loss.WeightedFocalLoss method) (neuro_morpho.model.loss.WeightedMap method) (neuro_morpho.model.transforms.DownSample method) (neuro_morpho.model.transforms.Norm2One method) (neuro_morpho.model.transforms.Standardize method) (neuro_morpho.model.unet.AttentionGroup method) (neuro_morpho.model.unet.ChannelAttention method) (neuro_morpho.model.unet.Conv2d method) (neuro_morpho.model.unet.Decoder method) (neuro_morpho.model.unet.DoubleConv2d method) (neuro_morpho.model.unet.Encoder method) (neuro_morpho.model.unet.SpatialAttention method) (neuro_morpho.model.unet.UNetModule method) (neuro_morpho.model.unet.UpConv2d method)

G

gamma (neuro_morpho.model.loss.WeightedFocalLoss attribute) generate_report() (in module neuro_morpho.reports.generator) generate_statistics() (in module neuro_morpho.reports.generator)

get_device() (in module neuro_morpho.util) get_tiling_attributes() (neuro_morpho.model.tiler.Tiler method) global_f1() (in module neuro_morpho.model.unet)

I

img_files (neuro_morpho.data.data_loader.NeuroMorphoDataset attribute)

L

LABEL_DIR (in module neuro_morpho.reports.report) LBL (in module neuro_morpho.model.metrics) lbl_files (neuro_morpho.data.data_loader.NeuroMorphoDataset attribute) load() (neuro_morpho.model.base.BaseModel method) (neuro_morpho.model.simple_baseline.SimpleBaseLine method) (neuro_morpho.model.unet.UNet method) load_checkpoint() (neuro_morpho.model.unet.UNet method) load_threshold() (neuro_morpho.model.unet.UNet method) log_code() (neuro_morpho.logging.base.Logger method) (neuro_morpho.logging.comet.CometLogger method) (neuro_morpho.logging.text.TextLogger method) log_dir (neuro_morpho.logging.text.TextLogger attribute) log_losses() (in module neuro_morpho.model.unet) log_metrics() (in module neuro_morpho.model.unet)

log_parameters() (neuro_morpho.logging.base.Logger method) (neuro_morpho.logging.comet.CometLogger method) (neuro_morpho.logging.text.TextLogger method) log_sample() (in module neuro_morpho.model.unet) log_scalar() (neuro_morpho.logging.base.Logger method) (neuro_morpho.logging.comet.CometLogger method) (neuro_morpho.logging.text.TextLogger method) log_triplet() (neuro_morpho.logging.base.Logger method) (neuro_morpho.logging.comet.CometLogger method) (neuro_morpho.logging.text.TextLogger method) Logger (class in neuro_morpho.logging.base) LOSS_FN (in module neuro_morpho.model.loss) loss_fn (neuro_morpho.model.loss.WeightedMap attribute) losses (neuro_morpho.model.loss.CombinedLoss attribute)

M

main() (in module neuro_morpho.cli) make_binary() (in module neuro_morpho.model.simple_baseline) masked_max() (neuro_morpho.model.breaks_analyzer.BreaksAnalyzer method) MAX_FIXABLE_DISTANCE (in module neuro_morpho.model.breaks_analyzer) max_pool (neuro_morpho.model.unet.ChannelAttention attribute) maybe_pbar() (in module neuro_morpho.model.unet) METRIC_FN (in module neuro_morpho.model.metrics) model (neuro_morpho.model.unet.UNet attribute) MODEL_OUT_DIR (in module neuro_morpho.reports.report) module neuro_morpho neuro_morpho.cli neuro_morpho.data neuro_morpho.data.data_loader neuro_morpho.logging neuro_morpho.logging.base neuro_morpho.logging.comet neuro_morpho.logging.plots neuro_morpho.logging.text neuro_morpho.model neuro_morpho.model.base neuro_morpho.model.breaks_analyzer neuro_morpho.model.loss neuro_morpho.model.metrics neuro_morpho.model.simple_baseline neuro_morpho.model.tiler neuro_morpho.model.transforms neuro_morpho.model.unet neuro_morpho.reports neuro_morpho.reports.generator neuro_morpho.reports.plots neuro_morpho.reports.report neuro_morpho.reports.stats neuro_morpho.run neuro_morpho.util

N

name (neuro_morpho.model.simple_baseline.SimpleBaseLine attribute) NAME_LOSS (in module neuro_morpho.model.loss) neuro_morpho module neuro_morpho.cli module neuro_morpho.data module neuro_morpho.data.data_loader module neuro_morpho.logging module neuro_morpho.logging.base module neuro_morpho.logging.comet module neuro_morpho.logging.plots module neuro_morpho.logging.text module neuro_morpho.model module neuro_morpho.model.base module neuro_morpho.model.breaks_analyzer module neuro_morpho.model.loss module

neuro_morpho.model.metrics module neuro_morpho.model.simple_baseline module neuro_morpho.model.tiler module neuro_morpho.model.transforms module neuro_morpho.model.unet module neuro_morpho.reports module neuro_morpho.reports.generator module neuro_morpho.reports.plots module neuro_morpho.reports.report module neuro_morpho.reports.stats module neuro_morpho.run module neuro_morpho.util module NeuroMorphoDataset (class in neuro_morpho.data.data_loader) noboxplot_summary() (in module neuro_morpho.reports.report) NOISE_LEVEL_PAT (in module neuro_morpho.reports.report) Norm2One (class in neuro_morpho.model.transforms)

P

percentile (neuro_morpho.model.simple_baseline.SimpleBaseLine attribute) plot_sabya() (in module neuro_morpho.reports.plots) plot_triplet() (in module neuro_morpho.logging.plots) pooling (neuro_morpho.model.unet.Encoder attribute) post_aug_x_transform (neuro_morpho.data.data_loader.NeuroMorphoDataset attribute) post_aug_y_transform (neuro_morpho.data.data_loader.NeuroMorphoDataset attribute) pre_aug_x_transform (neuro_morpho.data.data_loader.NeuroMorphoDataset attribute) pre_aug_y_transform (neuro_morpho.data.data_loader.NeuroMorphoDataset attribute)

PRED (in module neuro_morpho.model.loss) (in module neuro_morpho.model.metrics) predict() (neuro_morpho.model.base.BaseModel method) (neuro_morpho.model.simple_baseline.SimpleBaseLine method) predict_dir() (neuro_morpho.model.base.BaseModel method) (neuro_morpho.model.simple_baseline.SimpleBaseLine method) (neuro_morpho.model.unet.UNet method) predict_proba() (neuro_morpho.model.base.BaseModel method) (neuro_morpho.model.unet.UNet method)

R

reduction (neuro_morpho.model.loss.WeightedFocalLoss attribute) register_torch_transforms() (in module neuro_morpho.cli) relu (neuro_morpho.model.unet.Conv2d attribute) (neuro_morpho.model.unet.UpConv2d attribute)

REPORT_DIR (in module neuro_morpho.reports.report) report_fn (in module neuro_morpho.reports.report) run() (in module neuro_morpho.run)

S

save() (neuro_morpho.model.base.BaseModel method) (neuro_morpho.model.simple_baseline.SimpleBaseLine method) (neuro_morpho.model.unet.UNet method) save_checkpoint() (neuro_morpho.model.unet.UNet method) save_threshold() (neuro_morpho.model.unet.UNet method) sigmoid (neuro_morpho.model.unet.ChannelAttention attribute) (neuro_morpho.model.unet.SpatialAttention attribute) SigmoidDiceLoss (class in neuro_morpho.model.loss) SimpleBaseLine (class in neuro_morpho.model.simple_baseline)

skeleton_analysis() (in module neuro_morpho.reports.stats) SKELETON_STAT_FN (in module neuro_morpho.reports.stats) smooth (neuro_morpho.model.loss.SigmoidDiceLoss attribute) SpatialAttention (class in neuro_morpho.model.unet) Standardize (class in neuro_morpho.model.transforms) STAT_BRANCH_LENGTHS (in module neuro_morpho.reports.stats) STAT_N_BRANCHES (in module neuro_morpho.reports.stats) STAT_N_TIP_POINTS (in module neuro_morpho.reports.stats) STAT_TOTAL_LENGTH (in module neuro_morpho.reports.stats)

T

TARGET (in module neuro_morpho.model.loss) TextLogger (class in neuro_morpho.logging.text) tile_assembly (neuro_morpho.model.tiler.Tiler attribute) tile_image() (neuro_morpho.model.tiler.Tiler method)

tile_size (neuro_morpho.model.tiler.Tiler attribute) Tiler (class in neuro_morpho.model.tiler) train_step() (in module neuro_morpho.model.unet) transform_filename_to_group() (in module neuro_morpho.reports.report) triplet_dir (neuro_morpho.logging.text.TextLogger attribute)

U

UNet (class in neuro_morpho.model.unet)

UNetModule (class in neuro_morpho.model.unet) UpConv2d (class in neuro_morpho.model.unet)

V

val_step() (in module neuro_morpho.model.unet)

VALID_DISTANCES (in module neuro_morpho.reports.stats)

W

WeightedFocalLoss (class in neuro_morpho.model.loss)

WeightedMap (class in neuro_morpho.model.loss) weights (neuro_morpho.model.loss.CombinedLoss attribute)

X

x_coords (neuro_morpho.model.tiler.Tiler attribute)

Y

y_coords (neuro_morpho.model.tiler.Tiler attribute)