Index
Symbols
|
_
|
A
|
B
|
C
|
D
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
Symbols
**kwargs (tiramisu_brulee.experiment.seg.LesionSegLightningBase.forward parameter)
*args (tiramisu_brulee.experiment.seg.LesionSegLightningBase.forward parameter)
_
_model_num (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
A
add_arguments() (tiramisu_brulee.experiment.data.LesionSegDataModulePredictBase static method)
(tiramisu_brulee.experiment.data.LesionSegDataModuleTrain static method)
(tiramisu_brulee.experiment.data.Mixup static method)
add_io_arguments() (tiramisu_brulee.experiment.seg.LesionSegLightningBase static method)
add_model_arguments() (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu static method)
add_other_arguments() (tiramisu_brulee.experiment.seg.LesionSegLightningBase static method)
add_testing_arguments() (tiramisu_brulee.experiment.seg.LesionSegLightningBase static method)
add_training_arguments() (tiramisu_brulee.experiment.seg.LesionSegLightningBase static method)
almost_isbi15_score() (in module tiramisu_brulee.experiment.lesion_tools)
alpha (tiramisu_brulee.experiment.data.Mixup parameter)
append_num_to_filename() (in module tiramisu_brulee.experiment.util)
B
batch (tiramisu_brulee.experiment.seg.LesionSegLightningBase.on_predict_batch_end parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.predict_step parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.training_step parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.validation_step parameter)
batch_idx (tiramisu_brulee.experiment.seg.LesionSegLightningBase.on_predict_batch_end parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.predict_step parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.training_step parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.validation_step parameter)
batch_size (tiramisu_brulee.experiment.data.LesionSegDataModulePredictPatches parameter)
(tiramisu_brulee.experiment.data.LesionSegDataModulePredictWhole parameter)
(tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
betas (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
binary_combo_loss() (in module tiramisu_brulee.loss)
binary_focal_loss() (in module tiramisu_brulee.loss)
Bottleneck2d (class in tiramisu_brulee.model.dense)
Bottleneck3d (class in tiramisu_brulee.model.dense)
bottleneck_layers (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
BoundingBox3D (class in tiramisu_brulee.experiment.util)
C
check_dicom (tiramisu_brulee.experiment.data.csv_to_subjectlist parameter)
check_patch_size() (in module tiramisu_brulee.experiment.cli.common)
clean_segmentation() (in module tiramisu_brulee.experiment.lesion_tools)
combo_weight (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
commit (tiramisu_brulee.experiment.type.TiramisuBruleeInfo property)
configure_optimizers() (tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
crop_to_bbox() (tiramisu_brulee.experiment.util.BoundingBox3D method)
csv_to_subjectlist() (in module tiramisu_brulee.experiment.data)
D
dataloader_idx (tiramisu_brulee.experiment.seg.LesionSegLightningBase.on_predict_batch_end parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.predict_step parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.validation_step parameter)
decay_after (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
decay_rule() (tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
deeply_supervised_loss() (in module tiramisu_brulee.loss)
DenseBlock2d (class in tiramisu_brulee.model.dense)
DenseBlock3d (class in tiramisu_brulee.model.dense)
dice_loss() (in module tiramisu_brulee.loss)
dict_to_csv() (in module tiramisu_brulee.experiment.parse)
down_blocks (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
dropout_rate (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
F
file_path (class in tiramisu_brulee.experiment.type)
filename (tiramisu_brulee.experiment.data.csv_to_subjectlist parameter)
fill_holes (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
find_bbox() (tiramisu_brulee.experiment.util.BoundingBox3D static method)
first_conv_out_channels (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
fix_type_funcs() (in module tiramisu_brulee.experiment.parse)
focal_gamma (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
forward() (tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
from_batch() (tiramisu_brulee.experiment.util.BoundingBox3D class method)
from_csv() (tiramisu_brulee.experiment.data.LesionSegDataModulePredictWhole class method)
(tiramisu_brulee.experiment.data.LesionSegDataModuleTrain class method)
from_image() (tiramisu_brulee.experiment.util.BoundingBox3D class method)
from_string() (tiramisu_brulee.util.InitType class method)
G
gain (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
generate_predict_config_yaml() (in module tiramisu_brulee.experiment.parse)
generate_train_config_yaml() (in module tiramisu_brulee.experiment.parse)
get_best_model_path() (in module tiramisu_brulee.experiment.parse)
get_experiment_directory() (in module tiramisu_brulee.experiment.parse)
get_shape() (tiramisu_brulee.experiment.util.BoundingBox3D static method)
growth_rate (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
H
handle_fast_dev_run() (in module tiramisu_brulee.experiment.cli.common)
HE_NORMAL (tiramisu_brulee.util.InitType attribute)
HE_UNIFORM (tiramisu_brulee.util.InitType attribute)
hiddens (tiramisu_brulee.experiment.seg.LesionSegLightningBase.training_step parameter)
I
image_one_hot() (in module tiramisu_brulee.experiment.util)
in_channels (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
init_type (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
init_weights() (in module tiramisu_brulee.util)
InitType (class in tiramisu_brulee.util)
L
l1_segmentation_loss() (in module tiramisu_brulee.loss)
label_sampler (tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
learning_rate (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
LesionSegDataModulePredictBase (class in tiramisu_brulee.experiment.data)
LesionSegDataModulePredictPatches (class in tiramisu_brulee.experiment.data)
LesionSegDataModulePredictWhole (class in tiramisu_brulee.experiment.data)
LesionSegDataModuleTrain (class in tiramisu_brulee.experiment.data)
LesionSegLightningBase (class in tiramisu_brulee.experiment.seg)
LesionSegLightningTiramisu (class in tiramisu_brulee.experiment.seg)
loss_function (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
M
min_lesion_size (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
minmax_scale_batch() (in module tiramisu_brulee.experiment.util)
Mixup (class in tiramisu_brulee.experiment.data)
mixup (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
mixup_alpha (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
ModelNum (class in tiramisu_brulee.experiment.type)
module
tiramisu_brulee
tiramisu_brulee.experiment
tiramisu_brulee.experiment.cli
tiramisu_brulee.experiment.cli.common
tiramisu_brulee.experiment.cli.predict
tiramisu_brulee.experiment.cli.train
tiramisu_brulee.experiment.data
tiramisu_brulee.experiment.lesion_tools
tiramisu_brulee.experiment.parse
tiramisu_brulee.experiment.seg
tiramisu_brulee.experiment.type
tiramisu_brulee.experiment.util
tiramisu_brulee.loss
tiramisu_brulee.model
tiramisu_brulee.model.dense
tiramisu_brulee.model.tiramisu
tiramisu_brulee.util
mse_segmentation_loss() (in module tiramisu_brulee.loss)
N
n_epochs (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
network (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
network_dim (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
new_parse_type() (in module tiramisu_brulee.experiment.type)
none_string_to_none() (in module tiramisu_brulee.experiment.parse)
nonnegative_float (class in tiramisu_brulee.experiment.type)
nonnegative_int (class in tiramisu_brulee.experiment.type)
nonnegative_int_or_none_or_all (class in tiramisu_brulee.experiment.type)
NORMAL (tiramisu_brulee.util.InitType attribute)
num (tiramisu_brulee.experiment.type.ModelNum property)
num_classes (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
num_input (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
num_workers (tiramisu_brulee.experiment.data.LesionSegDataModulePredictPatches parameter)
(tiramisu_brulee.experiment.data.LesionSegDataModulePredictWhole parameter)
(tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
O
on_predict_batch_end() (tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
optimizer_idx (tiramisu_brulee.experiment.seg.LesionSegLightningBase.training_step parameter)
ORTHOGONAL (tiramisu_brulee.util.InitType attribute)
out_of (tiramisu_brulee.experiment.type.ModelNum property)
outputs (tiramisu_brulee.experiment.seg.LesionSegLightningBase.on_predict_batch_end parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.validation_epoch_end parameter)
P
parse_unknown_to_dict() (in module tiramisu_brulee.experiment.parse)
patch_overlap (tiramisu_brulee.experiment.data.LesionSegDataModulePredictPatches parameter)
patch_size (tiramisu_brulee.experiment.data.LesionSegDataModulePredictPatches parameter)
(tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
path_to_str() (in module tiramisu_brulee.experiment.parse)
pos_weight (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
positive_float (class in tiramisu_brulee.experiment.type)
positive_float_or_none (class in tiramisu_brulee.experiment.type)
positive_int (class in tiramisu_brulee.experiment.type)
positive_int_or_none (class in tiramisu_brulee.experiment.type)
positive_odd_int_or_none (class in tiramisu_brulee.experiment.type)
predict() (in module tiramisu_brulee.experiment.cli.predict)
predict_dataloader() (tiramisu_brulee.experiment.data.LesionSegDataModulePredictBase method)
predict_image() (in module tiramisu_brulee.experiment.cli.predict)
predict_probability (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
predict_step() (tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
probability_float (class in tiramisu_brulee.experiment.type)
probability_float_or_none (class in tiramisu_brulee.experiment.type)
pseudo3d_dim (tiramisu_brulee.experiment.data.LesionSegDataModulePredictPatches parameter)
(tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
pseudo3d_dims_setup() (in module tiramisu_brulee.experiment.cli.common)
pseudo3d_size (tiramisu_brulee.experiment.data.LesionSegDataModulePredictPatches parameter)
Q
queue_length (tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
R
remove_args() (in module tiramisu_brulee.experiment.parse)
reshape_for_broadcasting() (in module tiramisu_brulee.experiment.util)
rmsprop (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
S
samples_per_volume (tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
setup() (tiramisu_brulee.experiment.data.LesionSegDataModulePredictBase method)
(tiramisu_brulee.experiment.data.LesionSegDataModulePredictWhole method)
(tiramisu_brulee.experiment.data.LesionSegDataModuleTrain method)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
setup_log() (in module tiramisu_brulee.experiment.util)
soft_labels (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
spatial_augmentation (tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
split_filename() (in module tiramisu_brulee.experiment.util)
stage (tiramisu_brulee.experiment.data.LesionSegDataModulePredictBase.setup parameter)
(tiramisu_brulee.experiment.data.LesionSegDataModulePredictWhole.setup parameter)
(tiramisu_brulee.experiment.data.LesionSegDataModuleTrain.setup parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningBase.setup parameter)
strict (tiramisu_brulee.experiment.data.csv_to_subjectlist parameter)
subject (tiramisu_brulee.experiment.data.LesionSegDataModulePredictPatches parameter)
subjects (tiramisu_brulee.experiment.data.LesionSegDataModulePredictWhole parameter)
T
threshold (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
Tiramisu2d (class in tiramisu_brulee.model.tiramisu)
Tiramisu3d (class in tiramisu_brulee.model.tiramisu)
tiramisu_brulee
module
tiramisu_brulee.experiment
module
tiramisu_brulee.experiment.cli
module
tiramisu_brulee.experiment.cli.common
module
tiramisu_brulee.experiment.cli.predict
module
tiramisu_brulee.experiment.cli.train
module
tiramisu_brulee.experiment.data
module
tiramisu_brulee.experiment.lesion_tools
module
tiramisu_brulee.experiment.parse
module
tiramisu_brulee.experiment.seg
module
tiramisu_brulee.experiment.type
module
tiramisu_brulee.experiment.util
module
tiramisu_brulee.loss
module
tiramisu_brulee.model
module
tiramisu_brulee.model.dense
module
tiramisu_brulee.model.tiramisu
module
tiramisu_brulee.util
module
tiramisu_brulee_info() (in module tiramisu_brulee.experiment.cli.common)
TiramisuBruleeInfo (class in tiramisu_brulee.experiment.type)
to_np() (in module tiramisu_brulee.experiment.util)
train() (in module tiramisu_brulee.experiment.cli.train)
train_dataloader() (tiramisu_brulee.experiment.data.LesionSegDataModuleTrain method)
train_subject_list (tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
training_step() (tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
TransitionDown2d (class in tiramisu_brulee.model.dense)
TransitionDown3d (class in tiramisu_brulee.model.dense)
TransitionUp2d (class in tiramisu_brulee.model.dense)
TransitionUp3d (class in tiramisu_brulee.model.dense)
U
uncrop() (tiramisu_brulee.experiment.util.BoundingBox3D method)
uncrop_batch() (tiramisu_brulee.experiment.util.BoundingBox3D method)
up_blocks (tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
V
val_dataloader() (tiramisu_brulee.experiment.data.LesionSegDataModuleTrain method)
val_subject_list (tiramisu_brulee.experiment.data.LesionSegDataModuleTrain parameter)
validation_epoch_end() (tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
validation_step() (tiramisu_brulee.experiment.seg.LesionSegLightningBase method)
version (tiramisu_brulee.experiment.type.TiramisuBruleeInfo property)
W
weight_decay (tiramisu_brulee.experiment.seg.LesionSegLightningBase parameter)
(tiramisu_brulee.experiment.seg.LesionSegLightningTiramisu parameter)
X
XAVIER_NORMAL (tiramisu_brulee.util.InitType attribute)
tiramisu-brulee
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