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Echofilter 1.2.0 documentation
Contents:
Usage Guide
Installation
Command line interface primer
Quick Start
Inference operations
Pre-trained models
Citing Echofilter
Issues
Glossary
CLI Reference
echofilter
ev2csv
echofilter-train
echofilter-generate-shards
API Reference
echofilter package
echofilter.data package
echofilter.nn package
echofilter.nn.modules package
echofilter.optim package
echofilter.raw package
echofilter.ui package
echofilter.win package
Changelog
Module Index
Index
Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
A
Active data
Algorithm
aliases (echofilter.nn.wrapper.Echofilter attribute)
aside_fmt() (in module echofilter.ui.style)
AsideStyle (class in echofilter.ui.style)
AverageMeter (class in echofilter.optim.meters)
B
Bad data regions
bias (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
Bottom line
build_dataset() (in module echofilter.train)
C
cannonise_checkpoint_name() (in module echofilter.ui.checkpoints)
check_handles_visible() (echofilter.win.manager.WindowManager method)
check_if_windows() (in module echofilter.path)
Checkpoint
cli() (in module echofilter.ui.inference_cli)
ColorJitter (class in echofilter.data.transforms)
ConcatDataset (class in echofilter.data.dataset)
Conditional model
Conv2dSame (class in echofilter.nn.modules.conv)
count_lines() (in module echofilter.raw.loader)
count_parameters() (in module echofilter.nn.utils)
CSV
cumulative_sizes (echofilter.data.dataset.ConcatDataset attribute)
D
Dataset
datasets (echofilter.data.dataset.ConcatDataset attribute)
DedentTextHelpFormatter (class in echofilter.ui.formatters)
DepthwiseConv2d (class in echofilter.nn.modules.conv)
detach() (echofilter.nn.utils.TensorDict method)
detach_() (echofilter.nn.utils.TensorDict method)
determine_destination() (in module echofilter.path)
determine_file_path() (in module echofilter.path)
dilation (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
display() (echofilter.optim.meters.ProgressMeter method)
Down (class in echofilter.nn.unet)
Downfacing
download_checkpoint() (in module echofilter.ui.checkpoints)
dryrun_fmt() (in module echofilter.ui.style)
DryrunStyle (class in echofilter.ui.style)
E
Echofilter
echofilter
(class in echofilter.nn.wrapper)
module
echofilter.data
module
echofilter.data.dataset
module
echofilter.data.transforms
module
echofilter.data.utils
module
echofilter.ev2csv
module
echofilter.exe
echofilter.generate_shards
module
echofilter.inference
module
echofilter.nn
module
echofilter.nn.modules
module
echofilter.nn.modules.activations
module
echofilter.nn.modules.blocks
module
echofilter.nn.modules.conv
module
echofilter.nn.modules.pathing
module
echofilter.nn.modules.utils
module
echofilter.nn.unet
module
echofilter.nn.utils
module
echofilter.nn.wrapper
module
echofilter.optim
module
echofilter.optim.criterions
module
echofilter.optim.meters
module
echofilter.optim.schedulers
module
echofilter.optim.torch_backports
module
echofilter.optim.utils
module
echofilter.path
module
echofilter.plotting
module
echofilter.raw
module
echofilter.raw.loader
module
echofilter.raw.manipulate
module
echofilter.raw.metadata
module
echofilter.raw.shardloader
module
echofilter.raw.utils
module
echofilter.train
module
echofilter.ui
module
echofilter.ui.checkpoints
module
echofilter.ui.formatters
module
echofilter.ui.inference_cli
module
echofilter.ui.style
module
echofilter.ui.train_cli
module
echofilter.utils
module
echofilter.win
module
echofilter.win.ev
module
echofilter.win.manager
module
EchofilterLoss (class in echofilter.nn.wrapper)
Echogram
Echosounder
Echoview
ensure_axes_inverted() (in module echofilter.plotting)
Entrained air
error_fmt() (in module echofilter.ui.style)
error_message (class in echofilter.ui.style)
ErrorStyle (class in echofilter.ui.style)
EV file
ev2csv() (in module echofilter.ev2csv)
evdtstr2timestamp() (in module echofilter.raw.loader)
EVL
evl_loader() (in module echofilter.raw.loader)
evl_reader() (in module echofilter.raw.loader)
evl_writer() (in module echofilter.raw.loader)
EVR
evr_reader() (in module echofilter.raw.loader)
evr_writer() (in module echofilter.raw.loader)
extra_repr() (echofilter.nn.modules.activations.HardMish method)
(echofilter.nn.modules.activations.HardSwish method)
(echofilter.nn.modules.blocks.MBConv method)
(echofilter.nn.utils.TensorDict method)
F
fillholes2d() (in module echofilter.raw.utils)
find_nonzero_region_boundaries() (in module echofilter.raw.manipulate)
find_passive_data() (in module echofilter.raw.manipulate)
find_passive_data_v2() (in module echofilter.raw.manipulate)
find_window() (echofilter.win.manager.WindowManager method)
find_window_regex() (echofilter.win.manager.WindowManager method)
first_nonzero() (in module echofilter.utils)
fix_surface_line() (in module echofilter.raw.manipulate)
fixup_dataset_sample() (in module echofilter.data.dataset)
fixup_lines() (in module echofilter.raw.manipulate)
FlexibleConcat2d (class in echofilter.nn.modules.pathing)
FlexibleHelpFormatter (class in echofilter.ui.formatters)
format_parser_for_sphinx() (in module echofilter.ui.formatters)
forward() (echofilter.nn.modules.activations.HardMish method)
(echofilter.nn.modules.activations.HardSwish method)
(echofilter.nn.modules.activations.Mish method)
(echofilter.nn.modules.activations.Swish method)
(echofilter.nn.modules.blocks.MBConv method)
(echofilter.nn.modules.blocks.SqueezeExcite method)
(echofilter.nn.modules.conv.GaussianSmoothing method)
(echofilter.nn.modules.pathing.FlexibleConcat2d method)
(echofilter.nn.modules.pathing.ResidualConnect method)
(echofilter.nn.unet.Down method)
(echofilter.nn.unet.UNet method)
(echofilter.nn.unet.UNetBlock method)
(echofilter.nn.unet.Up method)
(echofilter.nn.wrapper.Echofilter method)
(echofilter.nn.wrapper.EchofilterLoss method)
foward() (echofilter.nn.modules.conv.SeparableConv2d method)
G
GaussianSmoothing (class in echofilter.nn.modules.conv)
generate_from_file() (in module echofilter.train)
generate_from_shards() (in module echofilter.train)
generate_from_transect() (in module echofilter.train)
generate_shard() (in module echofilter.generate_shards)
generate_shards() (in module echofilter.generate_shards)
get_checkpoint_list() (in module echofilter.ui.checkpoints)
get_color_palette() (in module echofilter.inference)
get_current_lr() (in module echofilter.optim.utils)
get_current_momentum() (in module echofilter.optim.utils)
get_default_cache_dir() (in module echofilter.ui.checkpoints)
get_default_checkpoint() (in module echofilter.ui.checkpoints)
get_indicator_onoffsets() (in module echofilter.utils)
get_lr() (echofilter.optim.schedulers.MesaOneCycleLR method)
(echofilter.optim.torch_backports.OneCycleLR method)
get_parser() (in module echofilter.ev2csv)
(in module echofilter.generate_shards)
(in module echofilter.ui.inference_cli)
(in module echofilter.ui.train_cli)
get_partition_data() (in module echofilter.raw.loader)
get_partition_list() (in module echofilter.raw.loader)
groups (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
H
HardMish (class in echofilter.nn.modules.activations)
HardSwish (class in echofilter.nn.modules.activations)
hexcolor2rgb8() (in module echofilter.inference)
hide() (echofilter.win.manager.WindowManager method)
hide_all() (echofilter.win.manager.WindowManager method)
highlight_fmt() (in module echofilter.ui.style)
HighlightStyle (class in echofilter.ui.style)
Hybrid model
I
import_lines_regions_to_ev() (in module echofilter.inference)
Inference
inference_transect() (in module echofilter.inference)
init_cnn() (in module echofilter.nn.modules.utils)
initialise_datapoints() (echofilter.data.dataset.ConcatDataset method)
(echofilter.data.dataset.TransectDataset method)
integrate_area_of_contour() (in module echofilter.raw.utils)
interp1d_preserve_nan() (in module echofilter.raw.utils)
J
join_transect() (in module echofilter.raw.manipulate)
K
kernel_size (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
L
last_nonzero() (in module echofilter.utils)
list_from_file() (in module echofilter.raw.loader)
ListCheckpoints (class in echofilter.ui.checkpoints)
ListColors (class in echofilter.ui.inference_cli)
load_checkpoint() (in module echofilter.ui.checkpoints)
load_decomposed_transect_mask() (in module echofilter.raw.manipulate)
load_transect_data() (in module echofilter.raw.loader)
load_transect_from_shards() (in module echofilter.raw.shardloader)
load_transect_from_shards_abs() (in module echofilter.raw.shardloader)
load_transect_from_shards_rel() (in module echofilter.raw.shardloader)
load_transect_segments_from_shards_abs() (in module echofilter.raw.shardloader)
load_transect_segments_from_shards_rel() (in module echofilter.raw.shardloader)
logavgexp() (in module echofilter.nn.utils)
M
Machine learning (ML)
main() (in module echofilter.ev2csv)
(in module echofilter.generate_shards)
(in module echofilter.ui.inference_cli)
(in module echofilter.ui.train_cli)
make_lines_from_mask() (in module echofilter.raw.manipulate)
make_lines_from_masked_csv() (in module echofilter.raw.manipulate)
mask_accuracy() (in module echofilter.optim.criterions)
mask_accuracy_with_logits() (in module echofilter.optim.criterions)
mask_active_fraction() (in module echofilter.optim.criterions)
mask_active_fraction_with_logits() (in module echofilter.optim.criterions)
mask_f1_score() (in module echofilter.optim.criterions)
mask_f1_score_with_logits() (in module echofilter.optim.criterions)
mask_jaccard_index() (in module echofilter.optim.criterions)
mask_jaccard_index_with_logits() (in module echofilter.optim.criterions)
mask_precision() (in module echofilter.optim.criterions)
mask_precision_with_logits() (in module echofilter.optim.criterions)
mask_recall() (in module echofilter.optim.criterions)
mask_recall_with_logits() (in module echofilter.optim.criterions)
maybe_open_echoview() (in module echofilter.win.ev)
MBConv (class in echofilter.nn.modules.blocks)
medfilt1d() (in module echofilter.raw.utils)
MesaOneCycleLR (class in echofilter.optim.schedulers)
meters_to_csv() (in module echofilter.train)
Mish (class in echofilter.nn.modules.activations)
mish() (in module echofilter.nn.modules.activations)
Mobile
mode() (in module echofilter.utils)
Model
module
echofilter
echofilter.data
echofilter.data.dataset
echofilter.data.transforms
echofilter.data.utils
echofilter.ev2csv
echofilter.generate_shards
echofilter.inference
echofilter.nn
echofilter.nn.modules
echofilter.nn.modules.activations
echofilter.nn.modules.blocks
echofilter.nn.modules.conv
echofilter.nn.modules.pathing
echofilter.nn.modules.utils
echofilter.nn.unet
echofilter.nn.utils
echofilter.nn.wrapper
echofilter.optim
echofilter.optim.criterions
echofilter.optim.meters
echofilter.optim.schedulers
echofilter.optim.torch_backports
echofilter.optim.utils
echofilter.path
echofilter.plotting
echofilter.raw
echofilter.raw.loader
echofilter.raw.manipulate
echofilter.raw.metadata
echofilter.raw.shardloader
echofilter.raw.utils
echofilter.train
echofilter.ui
echofilter.ui.checkpoints
echofilter.ui.formatters
echofilter.ui.inference_cli
echofilter.ui.style
echofilter.ui.train_cli
echofilter.utils
echofilter.win
echofilter.win.ev
echofilter.win.manager
N
Nearfield
Nearfield distance
Nearfield line
Neural network
Normalize (class in echofilter.data.transforms)
num_samples (echofilter.data.dataset.StratifiedRandomSampler property)
O
OneCycleLR (class in echofilter.optim.torch_backports)
open_ev_file() (in module echofilter.win.ev)
opencom() (in module echofilter.win.manager)
optimal_crop_depth() (in module echofilter.data.transforms)
OptimalCropDepth (class in echofilter.data.transforms)
order2kind (echofilter.data.transforms.Rescale attribute)
out_channels (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
output_padding (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
overwrite_fmt() (in module echofilter.ui.style)
OverwriteStyle (class in echofilter.ui.style)
P
pad1d() (in module echofilter.raw.utils)
pad_transect() (in module echofilter.raw.manipulate)
padding (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
padding_mode (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
parse_files_in_folders() (in module echofilter.path)
Passive data
Ping
plot_indicator_hatch() (in module echofilter.plotting)
plot_mask_hatch() (in module echofilter.plotting)
plot_transect() (in module echofilter.plotting)
plot_transect_predictions() (in module echofilter.plotting)
PointwiseConv2d (class in echofilter.nn.modules.conv)
progress_fmt() (in module echofilter.ui.style)
ProgressMeter (class in echofilter.optim.meters)
ProgressStyle (class in echofilter.ui.style)
R
RandomCropDepth (class in echofilter.data.transforms)
RandomCropWidth (class in echofilter.data.transforms)
RandomElasticGrid (class in echofilter.data.transforms)
RandomGridSampling (class in echofilter.data.transforms)
RandomReflection (class in echofilter.data.transforms)
recall_passive_edges() (in module echofilter.raw.metadata)
reduction (echofilter.nn.wrapper.EchofilterLoss attribute)
regions2mask() (in module echofilter.raw.loader)
remove_anomalies_1d() (in module echofilter.raw.manipulate)
remove_trailing_slash() (in module echofilter.raw.loader)
ReplaceNan (class in echofilter.data.transforms)
Rescale (class in echofilter.data.transforms)
reset (echofilter.ui.style.AsideStyle attribute)
(echofilter.ui.style.DryrunStyle attribute)
(echofilter.ui.style.ErrorStyle attribute)
(echofilter.ui.style.HighlightStyle attribute)
(echofilter.ui.style.OverwriteStyle attribute)
(echofilter.ui.style.ProgressStyle attribute)
(echofilter.ui.style.SkipStyle attribute)
(echofilter.ui.style.WarningStyle attribute)
reset() (echofilter.optim.meters.AverageMeter method)
(echofilter.win.manager.WindowManager method)
ResidualConnect (class in echofilter.nn.modules.pathing)
run_ev2csv() (in module echofilter.ev2csv)
run_inference() (in module echofilter.inference)
S
same_to_padding() (in module echofilter.nn.modules.utils)
Sample (model input)
(ping)
save_checkpoint() (in module echofilter.train)
seed_all() (in module echofilter.nn.utils)
segment_and_shard_transect() (in module echofilter.raw.shardloader)
SeparableConv2d (class in echofilter.nn.modules.conv)
set_foreground() (echofilter.win.manager.WindowManager method)
shard_transect() (in module echofilter.raw.shardloader)
show() (echofilter.win.manager.WindowManager method)
show_all() (echofilter.win.manager.WindowManager method)
ShowCacheDir (class in echofilter.ui.checkpoints)
skip_fmt() (in module echofilter.ui.style)
SkipStyle (class in echofilter.ui.style)
split_transect() (in module echofilter.raw.manipulate)
squash_gaps() (in module echofilter.raw.utils)
SqueezeExcite (class in echofilter.nn.modules.blocks)
start (echofilter.ui.style.AsideStyle attribute)
(echofilter.ui.style.DryrunStyle attribute)
(echofilter.ui.style.ErrorStyle attribute)
(echofilter.ui.style.HighlightStyle attribute)
(echofilter.ui.style.OverwriteStyle attribute)
(echofilter.ui.style.ProgressStyle attribute)
(echofilter.ui.style.SkipStyle attribute)
(echofilter.ui.style.WarningStyle attribute)
Stationary
str2actfnfactory() (in module echofilter.nn.modules.activations)
StratifiedRandomSampler (class in echofilter.data.dataset)
stride (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
Surface line
Sv
Swish (class in echofilter.nn.modules.activations)
swish() (in module echofilter.nn.modules.activations)
T
TensorDict (class in echofilter.nn.utils)
Test set
timestamp2evdtstr() (in module echofilter.raw.loader)
train() (in module echofilter.train)
train_epoch() (in module echofilter.train)
Training
training (echofilter.nn.modules.activations.HardMish attribute)
(echofilter.nn.modules.activations.HardSwish attribute)
(echofilter.nn.modules.activations.Mish attribute)
(echofilter.nn.modules.activations.Swish attribute)
(echofilter.nn.modules.blocks.MBConv attribute)
(echofilter.nn.modules.blocks.SqueezeExcite attribute)
(echofilter.nn.modules.conv.GaussianSmoothing attribute)
(echofilter.nn.modules.conv.SeparableConv2d attribute)
(echofilter.nn.modules.pathing.FlexibleConcat2d attribute)
(echofilter.nn.modules.pathing.ResidualConnect attribute)
(echofilter.nn.unet.Down attribute)
(echofilter.nn.unet.UNet attribute)
(echofilter.nn.unet.UNetBlock attribute)
(echofilter.nn.unet.Up attribute)
(echofilter.nn.wrapper.Echofilter attribute)
Training data
Training set
Transducer
transect_loader() (in module echofilter.raw.loader)
transect_reader() (in module echofilter.raw.loader)
TransectDataset (class in echofilter.data.dataset)
transposed (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
Turbulence
Turbulence line
U
UNet (class in echofilter.nn.unet)
UNetBlock (class in echofilter.nn.unet)
Up (class in echofilter.nn.unet)
update() (echofilter.optim.meters.AverageMeter method)
Upfacing
V
validate() (in module echofilter.train)
Validation set
W
warning_fmt() (in module echofilter.ui.style)
warning_message (class in echofilter.ui.style)
WarningStyle (class in echofilter.ui.style)
Water column
weight (echofilter.nn.modules.conv.Conv2dSame attribute)
(echofilter.nn.modules.conv.DepthwiseConv2d attribute)
(echofilter.nn.modules.conv.PointwiseConv2d attribute)
WindowManager (class in echofilter.win.manager)
worker_seed_fn() (in module echofilter.data.utils)
worker_staticseed_fn() (in module echofilter.data.utils)
write_lines_for_masked_csv() (in module echofilter.raw.manipulate)
write_transect_regions() (in module echofilter.raw.loader)
write_transect_shards() (in module echofilter.raw.shardloader)