ELEKTRONN2
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elektronn2.neuromancer package
elektronn2.training package
elektronn2.data package
elektronn2.utils package
elektronn2.malis package
ELEKTRONN2
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B
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C
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D
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E
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F
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H
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I
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K
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N
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O
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P
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Z
A
AbsLoss (class in elektronn2.neuromancer.loss)
AccumulationArray (class in elektronn2.utils.utils_basic)
activations() (elektronn2.neuromancer.model.Model method)
actstats() (elektronn2.neuromancer.model.Model method)
AdaDelta (class in elektronn2.neuromancer.optimiser)
AdaGrad (class in elektronn2.neuromancer.optimiser)
Adam (class in elektronn2.neuromancer.optimiser)
add_offset() (elektronn2.data.skeleton.Trace method)
(elektronn2.utils.utils_basic.AccumulationArray method)
add_scan_edges() (elektronn2.utils.d3viz.formatting.PyDotFormatter2 method)
add_timeticks() (in module elektronn2.utils.plotting)
addaxis() (elektronn2.neuromancer.graphutils.TaggedShape method)
AgentData (class in elektronn2.data.cnndata)
AggregateLoss (class in elektronn2.neuromancer.loss)
all_children (elektronn2.neuromancer.node_basic.Node attribute)
all_computational_cost (elektronn2.neuromancer.node_basic.Node attribute)
all_extra_updates (elektronn2.neuromancer.node_basic.Node attribute)
all_nontrainable_params (elektronn2.neuromancer.node_basic.Node attribute)
all_params (elektronn2.neuromancer.node_basic.Node attribute)
all_params_count (elektronn2.neuromancer.node_basic.Node attribute)
all_parents (elektronn2.neuromancer.node_basic.Node attribute)
all_trainable_params (elektronn2.neuromancer.node_basic.Node attribute)
alloc_shared_grads() (elektronn2.neuromancer.optimiser.Optimiser method)
append() (elektronn2.data.skeleton.Trace method)
(elektronn2.utils.utils_basic.AccumulationArray method)
(elektronn2.utils.utils_basic.CircularBuffer method)
(elektronn2.utils.utils_basic.DynamicKDT method)
append_serial() (elektronn2.data.skeleton.Trace method)
apply_activation() (in module elektronn2.neuromancer.computations)
apply_colors (elektronn2.utils.d3viz.formatting.PyDotFormatter2 attribute)
apply_except_axis() (in module elektronn2.neuromancer.computations)
ApplyFunc (class in elektronn2.neuromancer.node_basic)
as_floatX() (in module elektronn2.neuromancer.graphutils)
as_list() (in module elektronn2.utils.utils_basic)
avg_dist_self (elektronn2.data.skeleton.Trace attribute)
avg_dist_skel (elektronn2.data.skeleton.Trace attribute)
avg_seg_length (elektronn2.data.skeleton.Trace attribute)
B
BackgroundProc (class in elektronn2.training.parallelisation)
batch_normalisation_active (elektronn2.neuromancer.model.Model attribute)
BatchCreatorImage (class in elektronn2.data.cnndata)
bbox_off_sh_cent() (elektronn2.data.tracing_utils.CubeShape method)
bbox_wrt_input() (elektronn2.data.tracing_utils.CubeShape method)
bbox_wrt_self() (elektronn2.data.tracing_utils.CubeShape method)
BetaNLL (class in elektronn2.neuromancer.loss)
binary_nll() (in module elektronn2.training.trainutils)
BinaryNLL (class in elektronn2.neuromancer.loss)
bind_variable() (elektronn2.training.trainutils.Schedule method)
BlockedMultinoulliNLL (class in elektronn2.neuromancer.loss)
bmap_to_affgraph() (in module elektronn2.malis.malis_utils)
bmappred_to_affgraph() (in module elektronn2.malis.malis_utils)
C
cache (class in elektronn2.utils.utils_basic)
calc_max_dist_to_skels() (elektronn2.data.skeleton.SkeletonMFK method)
center_cubes() (in module elektronn2.data.image)
CG (class in elektronn2.neuromancer.optimiser)
change_logging_file() (in module elektronn2.config)
check() (elektronn2.data.tracing_utils.ShotgunRegistry method)
(elektronn2.utils.utils_basic.Timer method)
check_config() (elektronn2.training.trainutils.ExperimentConfig method)
CircularBuffer (class in elektronn2.utils.utils_basic)
clear() (elektronn2.utils.utils_basic.AccumulationArray method)
clear_last_dir() (elektronn2.neuromancer.optimiser.Optimiser method)
clone() (elektronn2.neuromancer.variables.ConstantParam method)
(elektronn2.neuromancer.variables.VariableParam method)
cnn_coord2lab_coord() (elektronn2.data.transformations.Transform method)
cnn_pred2lab_position() (elektronn2.data.transformations.Transform method)
cnncalculator() (in module elektronn2.utils.cnncalculator)
compile() (elektronn2.neuromancer.graphutils.make_func method)
compute_V_rand_N2() (in module elektronn2.malis.malis_utils)
Concat (class in elektronn2.neuromancer.node_basic)
confusion_table() (in module elektronn2.training.trainutils)
ConstantParam (class in elektronn2.neuromancer.variables)
Conv (class in elektronn2.neuromancer.neural)
conv() (in module elektronn2.neuromancer.computations)
convert_to_image() (elektronn2.data.traindata.MNISTData method)
copy() (elektronn2.neuromancer.graphutils.TaggedShape method)
create_cnn() (in module elektronn2.utils.legacy)
create_model() (in module elektronn2.tests.test_schedule_config)
createCVSplit() (elektronn2.data.traindata.Data method)
Crop (class in elektronn2.neuromancer.neural)
CubeShape (class in elektronn2.data.tracing_utils)
cut_slice() (elektronn2.data.knossos_array.KnossosArray method)
(elektronn2.data.knossos_array.KnossosArrayMulti method)
D
Data (class in elektronn2.data.traindata)
data (elektronn2.utils.utils_basic.AccumulationArray attribute)
(elektronn2.utils.utils_basic.CircularBuffer attribute)
debug_getcnnbatch() (elektronn2.training.trainer.TracingTrainer method)
(elektronn2.training.trainer.Trainer method)
debug_output_names (elektronn2.neuromancer.model.Model attribute)
delaxis() (elektronn2.neuromancer.graphutils.TaggedShape method)
designate_nodes() (elektronn2.neuromancer.model.Model method)
dict_to_pdnode() (in module elektronn2.utils.d3viz.formatting)
Dot (in module elektronn2.neuromancer.neural)
dot() (in module elektronn2.neuromancer.computations)
download() (elektronn2.data.traindata.MNISTData static method)
downsample_xy() (in module elektronn2.data.image)
dropout_rates (elektronn2.neuromancer.model.Model attribute)
DynamicKDT (class in elektronn2.utils.utils_basic)
E
elektronn2 (module)
elektronn2.config (module)
elektronn2.data (module)
elektronn2.data.cnndata (module)
elektronn2.data.image (module)
elektronn2.data.knossos_array (module)
elektronn2.data.skeleton (module)
elektronn2.data.tracing_utils (module)
elektronn2.data.traindata (module)
elektronn2.data.transformations (module)
elektronn2.malis (module)
elektronn2.malis.malis_utils (module)
elektronn2.malis.malisop (module)
elektronn2.neuromancer (module)
elektronn2.neuromancer.computations (module)
elektronn2.neuromancer.graphmanager (module)
elektronn2.neuromancer.graphutils (module)
elektronn2.neuromancer.loss (module)
elektronn2.neuromancer.model (module)
elektronn2.neuromancer.neural (module)
elektronn2.neuromancer.node_basic (module)
elektronn2.neuromancer.optimiser (module)
elektronn2.neuromancer.variables (module)
elektronn2.neuromancer.various (module)
elektronn2.tests (module)
elektronn2.tests.test_cnndata (module)
elektronn2.tests.test_data_image (module)
elektronn2.tests.test_malis (module)
elektronn2.tests.test_malis_fuck (module)
elektronn2.tests.test_neural (module)
elektronn2.tests.test_new_gm (module)
elektronn2.tests.test_new_split (module)
elektronn2.tests.test_restore (module)
elektronn2.tests.test_schedule (module)
elektronn2.tests.test_schedule_config (module)
elektronn2.tests.test_warping (module)
elektronn2.training (module)
elektronn2.training.parallelisation (module)
elektronn2.training.trainer (module)
elektronn2.training.trainutils (module)
elektronn2.utils (module)
elektronn2.utils.cnncalculator (module)
elektronn2.utils.d3viz (module)
elektronn2.utils.d3viz.formatting (module)
elektronn2.utils.gpu (module)
elektronn2.utils.legacy (module)
elektronn2.utils.plotting (module)
elektronn2.utils.ptk_completions (module)
elektronn2.utils.utils_basic (module)
ema (elektronn2.utils.utils_basic.AccumulationArray attribute)
embedfilters() (in module elektronn2.utils.plotting)
error_hist() (in module elektronn2.training.trainutils)
Errors() (in module elektronn2.neuromancer.loss)
escape_quotes() (in module elektronn2.utils.d3viz.formatting)
EuclideanDistance (class in elektronn2.neuromancer.loss)
eval_thresh() (in module elektronn2.training.trainutils)
evaluate() (in module elektronn2.training.trainutils)
evaluate_model_binary() (in module elektronn2.training.trainutils)
ExperimentConfig (class in elektronn2.training.trainutils)
ext_repr (elektronn2.neuromancer.graphutils.TaggedShape attribute)
F
FaithlessMerge (class in elektronn2.neuromancer.neural)
feature_names (elektronn2.neuromancer.node_basic.Node attribute)
find_joints() (elektronn2.data.skeleton.SkeletonMFK static method)
find_nearest() (in module elektronn2.training.trainutils)
find_nearest_trace() (elektronn2.data.tracing_utils.ShotgunRegistry method)
fov (elektronn2.neuromancer.graphutils.TaggedShape attribute)
fov_all_centered (elektronn2.neuromancer.graphutils.TaggedShape attribute)
fragmentpool() (in module elektronn2.neuromancer.computations)
fragments2dense() (in module elektronn2.neuromancer.computations)
FragmentsToDense (class in elektronn2.neuromancer.neural)
FromTensor (class in elektronn2.neuromancer.node_basic)
function_code() (elektronn2.neuromancer.graphmanager.GraphManager method)
G
GaussianNLL (class in elektronn2.neuromancer.loss)
GaussianRV (class in elektronn2.neuromancer.various)
GenericInput (class in elektronn2.neuromancer.node_basic)
get() (elektronn2.training.parallelisation.BackgroundProc method)
(elektronn2.training.parallelisation.SharedQ method)
get_cloesest_valid_patch_size() (in module elektronn2.utils.cnncalculator)
get_closest_node() (elektronn2.data.skeleton.SkeletonMFK method)
get_completions() (elektronn2.utils.ptk_completions.NumaCompleter method)
get_debug_outputs() (elektronn2.neuromancer.node_basic.Node method)
get_free_cpu_count() (in module elektronn2.utils.utils_basic)
get_free_gpu() (in module elektronn2.utils.gpu)
get_hull_branch_direc_cutoff() (elektronn2.data.skeleton.SkeletonMFK method)
get_hull_branch_dist_cutoff() (elektronn2.data.skeleton.SkeletonMFK method)
get_hull_points_inner() (elektronn2.data.skeleton.SkeletonMFK method)
get_hull_skel_direc_rel() (elektronn2.data.skeleton.SkeletonMFK method)
get_kdtree() (elektronn2.data.skeleton.SkeletonMFK method)
get_knn() (elektronn2.data.skeleton.SkeletonMFK method)
(elektronn2.utils.utils_basic.DynamicKDT method)
get_lock_names() (elektronn2.neuromancer.graphmanager.GraphManager static method)
get_loss_and_gradient() (elektronn2.data.skeleton.SkeletonMFK method)
get_newslice() (elektronn2.data.cnndata.AgentData method)
get_next_seed() (elektronn2.data.tracing_utils.ShotgunRegistry method)
get_node_props() (elektronn2.utils.d3viz.formatting.PyDotFormatter2 method)
get_param_values() (elektronn2.neuromancer.model.Model method)
(elektronn2.neuromancer.node_basic.Node method)
get_radius_nn() (elektronn2.utils.utils_basic.DynamicKDT method)
get_rotational_updates() (elektronn2.neuromancer.optimiser.Optimiser method)
get_scale_factor() (elektronn2.data.skeleton.SkeletonMFK static method)
(elektronn2.data.tracing_utils.Tracer method)
get_tracing_slice() (in module elektronn2.data.transformations)
get_valid_patch_sizes() (in module elektronn2.utils.cnncalculator)
get_value() (elektronn2.neuromancer.node_basic.InitialState_like method)
(elektronn2.neuromancer.node_basic.ValueNode method)
(elektronn2.neuromancer.variables.ConstantParam method)
getbatch() (elektronn2.data.cnndata.AgentData method)
(elektronn2.data.cnndata.BatchCreatorImage method)
(elektronn2.data.cnndata.GridData method)
(elektronn2.data.skeleton.SkeletonMFK method)
(elektronn2.data.traindata.Data method)
(elektronn2.data.traindata.MNISTData method)
(elektronn2.data.traindata.PianoData method)
(elektronn2.data.traindata.PianoData_perc method)
getinput_for_multioutput() (in module elektronn2.neuromancer.graphutils)
getskel() (elektronn2.data.cnndata.AgentData method)
global_lr (elektronn2.neuromancer.optimiser.Optimiser attribute)
global_mom (elektronn2.neuromancer.optimiser.Optimiser attribute)
global_weight_decay (elektronn2.neuromancer.optimiser.Optimiser attribute)
gradients() (elektronn2.neuromancer.model.Model method)
gradnet_rates (elektronn2.neuromancer.model.Model attribute)
gradstats() (elektronn2.neuromancer.model.Model method)
GraphManager (class in elektronn2.neuromancer.graphmanager)
GridData (class in elektronn2.data.cnndata)
GRU (class in elektronn2.neuromancer.neural)
H
h5load() (in module elektronn2.utils.utils_basic)
h5save() (in module elektronn2.utils.utils_basic)
hash_args() (elektronn2.utils.utils_basic.cache static method)
hastag() (elektronn2.neuromancer.graphutils.TaggedShape method)
HistoryTracker (class in elektronn2.training.trainutils)
I
ids2barriers() (in module elektronn2.data.image)
ImageAlign() (in module elektronn2.neuromancer.neural)
import_variable_from_file() (in module elektronn2.utils.utils_basic)
init_from_annotation() (elektronn2.data.skeleton.SkeletonMFK method)
initgpu() (in module elektronn2.utils.gpu)
InitialState_like (class in elektronn2.neuromancer.node_basic)
initweights() (in module elektronn2.neuromancer.variables)
Input (class in elektronn2.neuromancer.node_basic)
Input_like() (in module elektronn2.neuromancer.node_basic)
input_nodes (elektronn2.neuromancer.node_basic.Node attribute)
input_off_sh_cent() (elektronn2.data.tracing_utils.CubeShape method)
input_tensors (elektronn2.neuromancer.node_basic.Node attribute)
interpolate_bone() (elektronn2.data.skeleton.SkeletonMFK method)
interpolate_prop() (elektronn2.data.skeleton.SkeletonMFK method)
K
KDT (class in elektronn2.utils.utils_basic)
kernel_lists_from_node_descr() (in module elektronn2.neuromancer.model)
KnossosArray (class in elektronn2.data.knossos_array)
KnossosArrayMulti (class in elektronn2.data.knossos_array)
L
lab_coord2cnn_coord() (elektronn2.data.transformations.Transform method)
last_exec_time (elektronn2.neuromancer.node_basic.Node attribute)
levenshtein() (elektronn2.training.trainutils.ExperimentConfig class method)
load() (elektronn2.training.trainutils.HistoryTracker method)
load_data() (elektronn2.data.cnndata.AgentData method)
(elektronn2.data.cnndata.BatchCreatorImage method)
load_params_into_model() (in module elektronn2.utils.legacy)
loadhistorytracker() (in module elektronn2.training.trainutils)
local_exec_time (elektronn2.neuromancer.node_basic.Node attribute)
loss() (elektronn2.neuromancer.model.Model method)
loss_input_shapes (elektronn2.neuromancer.model.Model attribute)
loss_smooth (elektronn2.neuromancer.model.Model attribute)
lr (elektronn2.neuromancer.model.Model attribute)
LRN (class in elektronn2.neuromancer.neural)
LSTM (class in elektronn2.neuromancer.neural)
M
M_lin (elektronn2.data.transformations.Transform attribute)
M_lin_inv (elektronn2.data.transformations.Transform attribute)
make_affinities() (in module elektronn2.data.image)
make_dir() (elektronn2.training.trainutils.ExperimentConfig method)
make_dual() (elektronn2.neuromancer.neural.Conv method)
(elektronn2.neuromancer.neural.Perceptron method)
(elektronn2.neuromancer.neural.UpConv method)
make_func (class in elektronn2.neuromancer.graphutils)
make_grid (elektronn2.data.skeleton.SkeletonMFK attribute)
make_priorlayer() (elektronn2.neuromancer.various.GaussianRV method)
makeversiondir() (in module elektronn2.utils.utils_basic)
malis_weights() (in module elektronn2.malis.malisop)
MalisNLL (class in elektronn2.neuromancer.loss)
map_hull() (elektronn2.data.skeleton.SkeletonMFK method)
max() (elektronn2.utils.utils_basic.AccumulationArray method)
max_dist_skel (elektronn2.data.skeleton.Trace attribute)
maxout() (in module elektronn2.neuromancer.computations)
mean() (elektronn2.utils.utils_basic.AccumulationArray method)
(elektronn2.utils.utils_basic.CircularBuffer method)
measure_exectime() (elektronn2.neuromancer.node_basic.Node method)
measure_exectimes() (elektronn2.neuromancer.model.Model method)
mfp_offsets (elektronn2.neuromancer.graphutils.TaggedShape attribute)
min() (elektronn2.utils.utils_basic.AccumulationArray method)
min_dist_self (elektronn2.data.skeleton.Trace attribute)
min_normed_dist_self (elektronn2.data.skeleton.Trace attribute)
mixing (elektronn2.neuromancer.model.Model attribute)
mknhood2d() (in module elektronn2.malis.malis_utils)
mknhood3d() (in module elektronn2.malis.malis_utils)
mknhood3d_aniso() (in module elektronn2.malis.malis_utils)
MNISTData (class in elektronn2.data.traindata)
Model (class in elektronn2.neuromancer.model)
modelload() (in module elektronn2.neuromancer.model)
mom (elektronn2.neuromancer.model.Model attribute)
MultinoulliNLL (class in elektronn2.neuromancer.loss)
MultMerge (class in elektronn2.neuromancer.node_basic)
my_jit (class in elektronn2.utils.utils_basic)
my_quiver() (in module elektronn2.utils.plotting)
N
n_f (elektronn2.data.knossos_array.KnossosArray attribute)
ndim (elektronn2.neuromancer.graphutils.TaggedShape attribute)
new_cut_trace() (elektronn2.data.skeleton.Trace method)
new_reverted_trace() (elektronn2.data.skeleton.Trace method)
new_trace() (elektronn2.data.tracing_utils.ShotgunRegistry method)
Node (class in elektronn2.neuromancer.node_basic)
node_colors (elektronn2.utils.d3viz.formatting.PyDotFormatter2 attribute)
node_count (elektronn2.neuromancer.graphmanager.GraphManager attribute)
NumaCompleter (class in elektronn2.utils.ptk_completions)
O
offsets (elektronn2.neuromancer.graphutils.TaggedShape attribute)
OneHot (class in elektronn2.neuromancer.loss)
onscroll() (elektronn2.utils.plotting.Scroller method)
Optimiser (class in elektronn2.neuromancer.optimiser)
P
parallel_accum() (in module elektronn2.utils.utils_basic)
param_count (elektronn2.neuromancer.node_basic.Node attribute)
params_from_model_file() (in module elektronn2.neuromancer.model)
paramstats() (elektronn2.neuromancer.model.Model method)
Perceptron (class in elektronn2.neuromancer.neural)
performance_measure() (in module elektronn2.training.trainutils)
perturb_direciton() (elektronn2.data.tracing_utils.Tracer static method)
PianoData (class in elektronn2.data.traindata)
PianoData_perc (class in elektronn2.data.traindata)
pickleload() (in module elektronn2.utils.utils_basic)
picklesave() (in module elektronn2.utils.utils_basic)
plot() (elektronn2.data.skeleton.Trace method)
(elektronn2.neuromancer.graphmanager.GraphManager method)
(elektronn2.training.trainutils.HistoryTracker method)
(elektronn2.utils.utils_basic.Timer method)
plot_debug() (in module elektronn2.utils.plotting)
plot_debug_traces() (elektronn2.data.skeleton.SkeletonMFK method)
plot_exectimes() (in module elektronn2.utils.plotting)
plot_hist() (in module elektronn2.utils.plotting)
plot_hull() (elektronn2.data.skeleton.SkeletonMFK method)
plot_hull_inner() (elektronn2.data.skeleton.SkeletonMFK method)
plot_kde() (in module elektronn2.utils.plotting)
plot_mask_vol() (elektronn2.data.tracing_utils.ShotgunRegistry method)
plot_radii() (elektronn2.data.skeleton.SkeletonMFK method)
plot_regression() (in module elektronn2.utils.plotting)
plot_skel() (elektronn2.data.skeleton.SkeletonMFK method)
plot_theano_graph() (elektronn2.neuromancer.node_basic.Node method)
plot_trainingtarget() (in module elektronn2.utils.plotting)
plot_var() (in module elektronn2.utils.plotting)
plot_vec() (elektronn2.data.skeleton.SkeletonMFK method)
plot_vectors() (elektronn2.data.tracing_utils.Tracer static method)
point_potential() (elektronn2.data.skeleton.SkeletonMFK static method)
Pool (class in elektronn2.neuromancer.neural)
pooling() (in module elektronn2.neuromancer.computations)
predict() (elektronn2.neuromancer.model.Model method)
predict_and_write() (elektronn2.training.trainer.Trainer method)
predict_dense() (elektronn2.neuromancer.model.Model method)
(elektronn2.neuromancer.node_basic.Node method)
predict_ext() (elektronn2.neuromancer.model.Model method)
prediction_feature_names (elektronn2.neuromancer.model.Model attribute)
preload() (elektronn2.data.knossos_array.KnossosArray method)
(elektronn2.data.knossos_array.KnossosArrayMulti method)
pretty_string_ops() (in module elektronn2.utils.utils_basic)
pretty_string_time() (in module elektronn2.utils.utils_basic)
preview_slice() (elektronn2.training.trainer.Trainer method)
preview_slice_from_traindata() (elektronn2.training.trainer.Trainer method)
PyDotFormatter2 (class in elektronn2.utils.d3viz.formatting)
R
RampLoss (class in elektronn2.neuromancer.loss)
read_files() (elektronn2.data.cnndata.AgentData method)
(elektronn2.data.cnndata.BatchCreatorImage method)
read_user_config() (elektronn2.training.trainutils.ExperimentConfig method)
rebuild_model() (in module elektronn2.neuromancer.model)
register_debug_output_names() (elektronn2.training.trainutils.HistoryTracker method)
register_node() (elektronn2.neuromancer.graphmanager.GraphManager method)
register_split() (elektronn2.neuromancer.graphmanager.GraphManager method)
repair_fuckup() (elektronn2.neuromancer.optimiser.AdaDelta method)
(elektronn2.neuromancer.optimiser.AdaGrad method)
(elektronn2.neuromancer.optimiser.Adam method)
(elektronn2.neuromancer.optimiser.Optimiser method)
replace_patterns() (in module elektronn2.utils.d3viz.formatting)
rescale_fudge() (in module elektronn2.training.trainutils)
reset() (elektronn2.neuromancer.graphmanager.GraphManager method)
(elektronn2.training.parallelisation.BackgroundProc method)
Reshape (class in elektronn2.neuromancer.various)
restore() (elektronn2.neuromancer.graphmanager.GraphManager method)
roc_area() (in module elektronn2.training.trainutils)
run() (elektronn2.training.trainer.TracingTrainer method)
(elektronn2.training.trainer.TracingTrainerRNN method)
(elektronn2.training.trainer.Trainer method)
runlength (elektronn2.data.skeleton.Trace attribute)
S
sample_local_direction_iso() (elektronn2.data.skeleton.SkeletonMFK method)
sample_skel_point() (elektronn2.data.skeleton.SkeletonMFK method)
sample_tracing_direction_iso() (elektronn2.data.skeleton.SkeletonMFK method)
sample_tube_point() (elektronn2.data.skeleton.SkeletonMFK method)
save() (elektronn2.data.skeleton.SkeletonMFK method)
(elektronn2.data.skeleton.Trace method)
(elektronn2.neuromancer.model.Model method)
(elektronn2.training.trainutils.HistoryTracker method)
save_batch() (elektronn2.training.trainer.TracingTrainer static method)
save_to_kzip() (elektronn2.data.skeleton.Trace method)
Scan() (in module elektronn2.neuromancer.various)
Schedule (class in elektronn2.training.trainutils)
scroll_plot() (in module elektronn2.utils.plotting)
Scroller (class in elektronn2.utils.plotting)
seg_to_affgraph() (in module elektronn2.malis.malis_utils)
serialise() (elektronn2.neuromancer.graphmanager.GraphManager method)
set_opt_meta_params() (elektronn2.neuromancer.model.Model method)
(elektronn2.neuromancer.optimiser.Optimiser method)
set_param_values() (elektronn2.neuromancer.model.Model method)
(elektronn2.neuromancer.node_basic.Node method)
set_value() (elektronn2.neuromancer.variables.ConstantParam method)
(elektronn2.neuromancer.variables.VariableWeight method)
setlr() (elektronn2.neuromancer.optimiser.Optimiser class method)
setmom() (elektronn2.neuromancer.optimiser.Optimiser class method)
setvals() (elektronn2.utils.utils_basic.CircularBuffer method)
setwd() (elektronn2.neuromancer.optimiser.Optimiser class method)
SGD (class in elektronn2.neuromancer.optimiser)
shape (elektronn2.data.knossos_array.KnossosArray attribute)
(elektronn2.neuromancer.graphutils.TaggedShape attribute)
shapes (elektronn2.utils.d3viz.formatting.PyDotFormatter2 attribute)
SharedQ (class in elektronn2.training.parallelisation)
ShotgunRegistry (class in elektronn2.data.tracing_utils)
shrink_off_sh_cent() (elektronn2.data.tracing_utils.CubeShape method)
shutdown() (elektronn2.training.parallelisation.BackgroundProc method)
simple_cnn() (in module elektronn2.neuromancer.model)
sinks (elektronn2.neuromancer.graphmanager.GraphManager attribute)
SkeletonMFK (class in elektronn2.data.skeleton)
SkelGetBatch() (in module elektronn2.neuromancer.various)
SkelGridUpdate() (in module elektronn2.neuromancer.various)
SkelLoss() (in module elektronn2.neuromancer.various)
SkelLossRec (class in elektronn2.neuromancer.various)
SkelPrior (class in elektronn2.neuromancer.various)
sma() (in module elektronn2.utils.plotting)
smearbarriers() (in module elektronn2.data.image)
SobelizedLoss() (in module elektronn2.neuromancer.loss)
Softmax (class in elektronn2.neuromancer.loss)
softmax() (in module elektronn2.neuromancer.computations)
sort() (in module elektronn2.utils.d3viz.formatting)
sources (elektronn2.neuromancer.graphmanager.GraphManager attribute)
spatial_axes (elektronn2.neuromancer.graphutils.TaggedShape attribute)
spatial_shape (elektronn2.neuromancer.graphutils.TaggedShape attribute)
spatial_size (elektronn2.neuromancer.graphutils.TaggedShape attribute)
split() (in module elektronn2.neuromancer.node_basic)
split_uturns() (elektronn2.data.skeleton.Trace method)
SquaredLoss (class in elektronn2.neuromancer.loss)
startproc() (elektronn2.training.parallelisation.SharedQ method)
step_feedback() (elektronn2.data.skeleton.SkeletonMFK method)
step_grid_update() (elektronn2.data.skeleton.SkeletonMFK method)
strides (elektronn2.neuromancer.graphutils.TaggedShape attribute)
stripbatch_prod (elektronn2.neuromancer.graphutils.TaggedShape attribute)
stripnone (elektronn2.neuromancer.graphutils.TaggedShape attribute)
stripnone_prod (elektronn2.neuromancer.graphutils.TaggedShape attribute)
sum() (elektronn2.utils.utils_basic.AccumulationArray method)
summary() (elektronn2.utils.utils_basic.Timer method)
T
tag2index() (elektronn2.neuromancer.graphutils.TaggedShape method)
TaggedShape (class in elektronn2.neuromancer.graphutils)
tags (elektronn2.neuromancer.graphutils.TaggedShape attribute)
test_cnndata() (in module elektronn2.tests.test_cnndata)
test_data_image() (in module elektronn2.tests.test_data_image)
test_malis() (in module elektronn2.tests.test_malis)
test_malis_fuck() (in module elektronn2.tests.test_malis_fuck)
test_model() (elektronn2.training.trainer.TracingTrainer method)
(elektronn2.training.trainer.TracingTrainerRNN method)
(elektronn2.training.trainer.Trainer method)
test_neural() (in module elektronn2.tests.test_neural)
test_new_gm() (in module elektronn2.tests.test_new_gm)
test_restore() (in module elektronn2.tests.test_restore)
test_run() (elektronn2.neuromancer.node_basic.Node method)
test_run_prediction() (elektronn2.neuromancer.model.Model method)
test_schedule() (in module elektronn2.tests.test_schedule)
test_schedule_config() (in module elektronn2.tests.test_schedule_config)
test_warping() (in module elektronn2.tests.test_warping)
time_per_step (elektronn2.neuromancer.model.Model attribute)
timeit (class in elektronn2.utils.utils_basic)
TimeoutError
Timer (class in elektronn2.utils.utils_basic)
to_array() (elektronn2.data.transformations.Transform method)
tortuosity() (elektronn2.data.skeleton.Trace method)
total_exec_time (elektronn2.neuromancer.node_basic.Node attribute)
Trace (class in elektronn2.data.skeleton)
trace() (elektronn2.data.tracing_utils.Tracer method)
trace_to_kzip() (in module elektronn2.data.skeleton)
Tracer (class in elektronn2.data.tracing_utils)
TracingTrainer (class in elektronn2.training.trainer)
TracingTrainerRNN (class in elektronn2.training.trainer)
trafo_from_array() (in module elektronn2.data.transformations)
Trainer (class in elektronn2.training.trainer)
trainingstep() (elektronn2.neuromancer.model.Model method)
Transform (class in elektronn2.data.transformations)
U
unique_rows() (in module elektronn2.utils.utils_basic)
unpooling() (in module elektronn2.neuromancer.computations)
unpooling_nd() (in module elektronn2.neuromancer.computations)
UpConv (class in elektronn2.neuromancer.neural)
upconv() (in module elektronn2.neuromancer.computations)
UpConvMerge() (in module elektronn2.neuromancer.neural)
update() (elektronn2.training.trainutils.Schedule method)
(elektronn2.utils.plotting.Scroller method)
update_debug_outputs() (elektronn2.training.trainutils.HistoryTracker method)
update_history() (elektronn2.training.trainutils.HistoryTracker method)
update_mask() (elektronn2.data.tracing_utils.ShotgunRegistry method)
update_regression() (elektronn2.training.trainutils.HistoryTracker method)
update_timeline() (elektronn2.training.trainutils.HistoryTracker method)
updatefov() (elektronn2.neuromancer.graphutils.TaggedShape method)
updatemfp_offsets() (elektronn2.neuromancer.graphutils.TaggedShape method)
updates (elektronn2.neuromancer.variables.ConstantParam attribute)
(elektronn2.neuromancer.variables.VariableParam attribute)
updateshape() (elektronn2.neuromancer.graphutils.TaggedShape method)
updatestrides() (elektronn2.neuromancer.graphutils.TaggedShape method)
upsampling() (in module elektronn2.neuromancer.computations)
upsampling_nd() (in module elektronn2.neuromancer.computations)
user_input() (in module elektronn2.training.trainutils)
V
ValueNode (class in elektronn2.neuromancer.node_basic)
VariableParam (class in elektronn2.neuromancer.variables)
VariableWeight (class in elektronn2.neuromancer.variables)
visualise_model() (in module elektronn2.utils.d3viz.formatting)
W
warning_shown (elektronn2.utils.utils_basic.KDT attribute)
warp_cut() (elektronn2.data.cnndata.BatchCreatorImage method)
warp_slice() (in module elektronn2.data.transformations)
warp_stats (elektronn2.data.cnndata.BatchCreatorImage attribute)
WarpingOOBError
watershed_from_affgraph() (in module elektronn2.malis.malis_utils)
wd (elektronn2.neuromancer.model.Model attribute)
Z
zeropad() (elektronn2.data.tracing_utils.Tracer static method)
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