Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
J
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
A
add_neurons() (snudda.place.place.SnuddaPlace method)
all_neuron_names() (snudda.place.place.SnuddaPlace method)
all_neuron_positions() (snudda.place.place.SnuddaPlace method)
all_neuron_rotations() (snudda.place.place.SnuddaPlace method)
apply() (snudda.neurons.neuron_prototype.NeuronPrototype method)
B
BenchmarkLogging (class in snudda.utils.benchmark_logging)
big_merge_helper() (snudda.detect.prune.SnuddaPrune method)
buffer_merge_write() (snudda.detect.prune.SnuddaPrune method)
C
cache_exist() (snudda.neurons.neuron_morphology.NeuronMorphology method)
(snudda.place.region_mesh.RegionMesh method)
check_hyper_voxel_integrity() (snudda.detect.prune.SnuddaPrune method)
check_inside() (snudda.place.region_mesh.RegionMesh method)
check_network_config_integrity() (snudda.detect.prune.SnuddaPrune method)
check_sorted() (snudda.input.input.SnuddaInput method)
clean_up_merge_files() (snudda.detect.prune.SnuddaPrune method)
clean_up_merge_read_buffers() (snudda.detect.prune.SnuddaPrune method)
cleanup() (in module snudda.utils.cleanup)
(snudda.detect.prune.SnuddaPrune method)
cleanup_memory() (in module snudda.utils.cleanup)
clone() (snudda.neurons.neuron_morphology.NeuronMorphology method)
(snudda.neurons.neuron_prototype.NeuronPrototype method)
close() (snudda.utils.load.SnuddaLoad method)
(snudda.utils.reposition_neurons.RepositionNeurons method)
cluster_neurons() (snudda.place.place.SnuddaPlace method)
cluster_synapses() (snudda.neurons.neuron_morphology.NeuronMorphology method)
combine_files() (snudda.detect.prune.SnuddaPrune method)
compartment_length() (snudda.neurons.neuron_morphology.NeuronMorphology method)
complete_pruning_info() (snudda.detect.prune.SnuddaPrune static method)
connect_projection_helper() (snudda.detect.project.SnuddaProject method)
create_connection_matrix() (snudda.utils.export_connection_matrix.SnuddaExportConnectionMatrix method)
create_cube_mesh() (in module snudda.place.create_cube_mesh)
create_lookup_table() (snudda.detect.detect.SnuddaDetect static method)
create_slice_mesh() (in module snudda.place.create_slice_mesh)
create_spike_matrix() (snudda.input.input.SnuddaInput static method)
cull_spikes() (snudda.input.input.SnuddaInput static method)
D
default() (snudda.utils.numpy_encoder.NumpyEncoder method)
define_density() (snudda.place.region_mesh.RegionMesh method)
define_population_units() (snudda.place.place.SnuddaPlace method)
define_structure() (snudda.init.init.SnuddaInit method)
delete_old_merge() (snudda.detect.detect.SnuddaDetect method)
dendrite_input_locations() (snudda.input.input.SnuddaInput method)
(snudda.neurons.neuron_morphology.NeuronMorphology method)
dendrite_input_locations_helper() (snudda.neurons.neuron_morphology.NeuronMorphology method)
detect() (snudda.detect.detect.SnuddaDetect method)
detect_gap_junctions() (snudda.detect.detect.SnuddaDetect method)
detect_synapses() (snudda.detect.detect.SnuddaDetect method)
distribute_neurons() (snudda.detect.detect.SnuddaDetect method)
distribute_neurons_parallel() (snudda.detect.detect.SnuddaDetect method)
E
estimate_correlation() (snudda.input.input.SnuddaInput static method)
export_voxel_visualisation_csv() (snudda.detect.detect.SnuddaDetect method)
extract_neurons() (snudda.utils.load.SnuddaLoad static method)
F
file_row_lookup_iterator_subset() (snudda.detect.prune.SnuddaPrune method)
fill_voxels_axon() (snudda.detect.detect.SnuddaDetect method)
fill_voxels_dend() (snudda.detect.detect.SnuddaDetect method)
fill_voxels_soma() (snudda.detect.detect.SnuddaDetect method)
filter_neurons_synapses() (snudda.utils.cut.SnuddaCut method)
find_gap_junctions() (snudda.utils.load.SnuddaLoad method)
find_min_max_coord() (snudda.detect.detect.SnuddaDetect method)
find_min_max_coord_parallel() (snudda.detect.detect.SnuddaDetect method)
find_radius() (snudda.neurons.neuron_morphology.NeuronMorphology method)
find_ranges() (snudda.detect.prune.SnuddaPrune method)
find_synapses() (snudda.utils.load.SnuddaLoad method)
find_synapses_slow() (snudda.utils.load.SnuddaLoad method)
G
gap_junction_iterator() (snudda.utils.load.SnuddaLoad method)
gather_neuron_synapses() (snudda.detect.prune.SnuddaPrune method)
generate() (snudda.input.input.SnuddaInput method)
generate_hyper_voxel_random_seeds() (snudda.detect.detect.SnuddaDetect method)
generate_neuron_distribution_random_seeds() (snudda.detect.detect.SnuddaDetect method)
generate_poisson_spikes_helper() (snudda.input.input.SnuddaInput method)
generate_seeds() (snudda.input.input.SnuddaInput method)
generate_spikes_function() (snudda.input.input.SnuddaInput method)
generate_spikes_function_helper() (snudda.input.input.SnuddaInput method)
get_centre_neurons_iterator() (snudda.utils.load.SnuddaLoad method)
get_hyper_voxel_axon_points() (snudda.detect.detect.SnuddaDetect method)
get_hyper_voxel_list() (snudda.detect.prune.SnuddaPrune method)
get_master_node_rng() (snudda.input.input.SnuddaInput method)
get_merge_info() (snudda.detect.prune.SnuddaPrune method)
get_merge_info_helper() (snudda.detect.prune.SnuddaPrune method)
get_modulation_parameters() (snudda.neurons.neuron_prototype.NeuronPrototype method)
get_morphologies() (snudda.init.init.SnuddaInit method)
get_morphology() (snudda.neurons.neuron_prototype.NeuronPrototype method)
get_network_name() (snudda.utils.benchmark_logging.BenchmarkLogging static method)
get_neuron_distribution_history() (snudda.detect.detect.SnuddaDetect method)
get_neuron_id_of_type() (snudda.utils.load.SnuddaLoad method)
get_neuron_id_with_name() (snudda.utils.load.SnuddaLoad method)
get_neuron_random_seeds() (snudda.detect.prune.SnuddaPrune method)
get_number_of_workers() (snudda.utils.benchmark_logging.BenchmarkLogging method)
get_parameters() (snudda.neurons.neuron_prototype.NeuronPrototype method)
get_population_unit_members() (snudda.utils.load.SnuddaLoad method)
get_rotations() (snudda.place.rotation.SnuddaRotate method)
get_snudda_data() (in module snudda.utils.snudda_path)
get_subset() (snudda.place.region_mesh.RegionMesh method)
I
includes_gap_junctions() (snudda.detect.detect.SnuddaDetect method)
init_population_units() (snudda.place.place.SnuddaPlace method)
inner_voxel_volume() (snudda.place.region_mesh.RegionMesh method)
instantiate() (snudda.neurons.neuron_prototype.NeuronPrototype method)
J
jitter_spikes() (snudda.input.input.SnuddaInput static method)
L
load_cache() (snudda.neurons.neuron_morphology.NeuronMorphology method)
(snudda.place.region_mesh.RegionMesh method)
load_config_file() (snudda.utils.load.SnuddaLoad method)
load_hdf5() (snudda.utils.load.SnuddaLoad method)
load_info() (snudda.neurons.neuron_prototype.NeuronPrototype method)
load_mesh() (snudda.place.region_mesh.RegionMesh method)
load_neuron() (snudda.detect.detect.SnuddaDetect method)
(snudda.utils.load.SnuddaLoad method)
load_neuron_morphology() (snudda.neurons.neuron_morphology.NeuronMorphology method)
load_pruning_information() (snudda.detect.prune.SnuddaPrune method)
load_rotation_field() (snudda.place.rotation.SnuddaRotate static method)
load_swc() (snudda.neurons.neuron_morphology.NeuronMorphology method)
M
make_correlated_spikes() (snudda.input.input.SnuddaInput method)
make_input_helper_parallel() (snudda.input.input.SnuddaInput method)
make_input_helper_serial() (snudda.input.input.SnuddaInput method)
make_neuron_input_parallel() (snudda.input.input.SnuddaInput method)
make_population_unit_spike_trains() (snudda.input.input.SnuddaInput method)
make_type_numbering() (snudda.detect.prune.SnuddaPrune method)
make_uncorrelated_spikes() (snudda.input.input.SnuddaInput method)
mark_borders() (snudda.place.region_mesh.RegionMesh method)
memory_status() (in module snudda.utils.memory)
mix_fraction_of_spikes() (snudda.input.input.SnuddaInput static method)
mix_fraction_of_spikes_OLD() (snudda.input.input.SnuddaInput static method)
mix_spikes() (snudda.input.input.SnuddaInput static method)
module
snudda.detect.detect
snudda.detect.project
snudda.detect.prune
snudda.init.init
snudda.input.input
snudda.neurons.neuron_model_extended
snudda.neurons.neuron_morphology
snudda.neurons.neuron_prototype
snudda.place.create_cube_mesh
snudda.place.create_slice_mesh
snudda.place.place
snudda.place.region_mesh
snudda.place.rotation
snudda.simulate
snudda.utils.benchmark_logging
snudda.utils.cleanup
snudda.utils.cut
snudda.utils.export_connection_matrix
snudda.utils.load
snudda.utils.memory
snudda.utils.numpy_encoder
snudda.utils.reposition_neurons
snudda.utils.snudda_path
N
NeuronMorphology (class in snudda.neurons.neuron_morphology)
NeuronPrototype (class in snudda.neurons.neuron_prototype)
no_axon_points_sphere() (snudda.detect.detect.SnuddaDetect method)
no_axon_points_xyz() (snudda.detect.detect.SnuddaDetect method)
NumpyEncoder (class in snudda.utils.numpy_encoder)
O
open_hyper_voxel() (snudda.detect.prune.SnuddaPrune method)
open_input_file() (snudda.utils.cut.SnuddaCut method)
open_work_history_file() (snudda.detect.prune.SnuddaPrune method)
P
parallel_process_hyper_voxels() (snudda.detect.detect.SnuddaDetect method)
parse_config() (snudda.place.place.SnuddaPlace method)
parse_config_file() (snudda.place.rotation.SnuddaRotate method)
place() (snudda.neurons.neuron_morphology.NeuronMorphology method)
(snudda.place.place.SnuddaPlace method)
(snudda.utils.reposition_neurons.RepositionNeurons method)
place_synapses_no_axon() (snudda.detect.detect.SnuddaDetect method)
plot_cut() (snudda.utils.cut.SnuddaCut method)
plot_hyper_voxel() (snudda.detect.detect.SnuddaDetect method)
plot_neuron() (snudda.neurons.neuron_morphology.NeuronMorphology method)
plot_neurons() (snudda.place.region_mesh.RegionMesh method)
plot_neurons_in_hyper_voxel() (snudda.detect.detect.SnuddaDetect method)
plot_spikes() (snudda.input.input.SnuddaInput method)
plot_struct() (snudda.place.region_mesh.RegionMesh method)
population_unit_density_labeling() (snudda.place.place.SnuddaPlace method)
pre_compute() (snudda.place.region_mesh.RegionMesh method)
process_hyper_voxel() (snudda.detect.detect.SnuddaDetect method)
project() (snudda.detect.project.SnuddaProject method)
prune() (snudda.detect.prune.SnuddaPrune method)
prune_synapses() (snudda.detect.prune.SnuddaPrune method)
prune_synapses_helper() (snudda.detect.prune.SnuddaPrune method)
prune_synapses_parallel() (snudda.detect.prune.SnuddaPrune method)
R
rand_rotation_matrix() (snudda.neurons.neuron_morphology.NeuronMorphology static method)
random_labeling() (snudda.place.place.SnuddaPlace method)
random_z_rotate() (snudda.place.rotation.SnuddaRotate static method)
raster_plot() (snudda.input.input.SnuddaInput static method)
ray_casting() (snudda.place.region_mesh.RegionMesh method)
read_input_config_file() (snudda.input.input.SnuddaInput method)
read_network_config_file() (snudda.input.input.SnuddaInput method)
read_neuron_positions() (snudda.detect.detect.SnuddaDetect method)
(snudda.detect.project.SnuddaProject method)
read_prototypes() (snudda.detect.detect.SnuddaDetect method)
(snudda.detect.project.SnuddaProject method)
RegionMesh (class in snudda.place.region_mesh)
remove_empty() (snudda.detect.detect.SnuddaDetect method)
replace_connectivity() (snudda.init.init.SnuddaInit method)
RepositionNeurons (class in snudda.utils.reposition_neurons)
resize_hyper_voxel_synapses_matrix() (snudda.detect.detect.SnuddaDetect method)
rotation_matrix_from_vectors() (snudda.place.rotation.SnuddaRotate static method)
S
save_cache() (snudda.neurons.neuron_morphology.NeuronMorphology method)
(snudda.place.region_mesh.RegionMesh method)
save_merge_info() (snudda.detect.prune.SnuddaPrune method)
save_neuron_distribution_history() (snudda.detect.detect.SnuddaDetect method)
set_axon_voxel_radial_density() (snudda.neurons.neuron_morphology.NeuronMorphology method)
set_axon_voxel_xyz_density() (snudda.neurons.neuron_morphology.NeuronMorphology method)
set_modulation_id() (snudda.utils.reposition_neurons.RepositionNeurons method)
set_modulation_key() (snudda.utils.reposition_neurons.RepositionNeurons method)
set_morphology_id() (snudda.utils.reposition_neurons.RepositionNeurons method)
set_morphology_key() (snudda.utils.reposition_neurons.RepositionNeurons method)
set_parameter_id() (snudda.utils.reposition_neurons.RepositionNeurons method)
set_parameter_key() (snudda.utils.reposition_neurons.RepositionNeurons method)
set_scratch_path() (snudda.detect.prune.SnuddaPrune method)
setup_hyper_voxel() (snudda.detect.detect.SnuddaDetect method)
setup_log() (snudda.detect.detect.SnuddaDetect method)
setup_merge_file() (snudda.detect.prune.SnuddaPrune method)
setup_output_file() (snudda.detect.prune.SnuddaPrune method)
(snudda.utils.cut.SnuddaCut method)
setup_parallel() (snudda.detect.detect.SnuddaDetect method)
(snudda.detect.prune.SnuddaPrune method)
(snudda.input.input.SnuddaInput method)
(snudda.place.region_mesh.RegionMesh method)
setup_place_neurons() (snudda.place.region_mesh.RegionMesh method)
setup_process_hyper_voxel_state_history() (snudda.detect.detect.SnuddaDetect method)
setup_voxel_filter() (snudda.place.region_mesh.RegionMesh method)
setup_voxel_list() (snudda.place.region_mesh.RegionMesh method)
setup_work_history() (snudda.detect.detect.SnuddaDetect method)
snudda.detect.detect
module
snudda.detect.project
module
snudda.detect.prune
module
snudda.init.init
module
snudda.input.input
module
snudda.neurons.neuron_model_extended
module
snudda.neurons.neuron_morphology
module
snudda.neurons.neuron_prototype
module
snudda.place.create_cube_mesh
module
snudda.place.create_slice_mesh
module
snudda.place.place
module
snudda.place.region_mesh
module
snudda.place.rotation
module
snudda.simulate
module
snudda.utils.benchmark_logging
module
snudda.utils.cleanup
module
snudda.utils.cut
module
snudda.utils.export_connection_matrix
module
snudda.utils.load
module
snudda.utils.memory
module
snudda.utils.numpy_encoder
module
snudda.utils.reposition_neurons
module
snudda.utils.snudda_path
module
snudda_isdir() (in module snudda.utils.snudda_path)
snudda_isfile() (in module snudda.utils.snudda_path)
snudda_load_cli() (in module snudda.utils.load)
snudda_parse_path() (in module snudda.utils.snudda_path)
snudda_path_exists() (in module snudda.utils.snudda_path)
snudda_simplify_path() (in module snudda.utils.snudda_path)
SnuddaCut (class in snudda.utils.cut)
SnuddaDetect (class in snudda.detect.detect)
SnuddaExportConnectionMatrix (class in snudda.utils.export_connection_matrix)
SnuddaInit (class in snudda.init.init)
SnuddaInput (class in snudda.input.input)
SnuddaLoad (class in snudda.utils.load)
SnuddaPlace (class in snudda.place.place)
SnuddaProject (class in snudda.detect.project)
SnuddaPrune (class in snudda.detect.prune)
SnuddaRotate (class in snudda.place.rotation)
soma_inside() (snudda.utils.cut.SnuddaCut method)
sort_gap_junctions() (snudda.detect.detect.SnuddaDetect method)
sort_neurons() (snudda.place.place.SnuddaPlace method)
sort_remaining_by_size() (snudda.detect.detect.SnuddaDetect method)
sort_synapses() (snudda.detect.detect.SnuddaDetect method)
start_timer() (snudda.utils.benchmark_logging.BenchmarkLogging method)
stop_timer() (snudda.utils.benchmark_logging.BenchmarkLogging method)
synapse_iterator() (snudda.utils.load.SnuddaLoad method)
synapse_set_iterator() (snudda.detect.prune.SnuddaPrune static method)
synapses_inside() (snudda.utils.cut.SnuddaCut method)
T
test_plot() (snudda.place.region_mesh.RegionMesh method)
test_plot_cached() (snudda.place.region_mesh.RegionMesh method)
to_str() (snudda.utils.load.SnuddaLoad static method)
U
update_padding_mask() (snudda.place.region_mesh.RegionMesh method)
update_process_hyper_voxel_state() (snudda.detect.detect.SnuddaDetect method)
update_random_pool() (snudda.place.region_mesh.RegionMesh method)
V
verify_correlation() (snudda.input.input.SnuddaInput method)
verify_d_min() (snudda.place.region_mesh.RegionMesh method)
verify_inside() (snudda.place.region_mesh.RegionMesh method)
W
write() (snudda.detect.project.SnuddaProject method)
write_cut_slice() (snudda.utils.cut.SnuddaCut method)
write_data() (snudda.place.place.SnuddaPlace method)
write_hdf5() (snudda.input.input.SnuddaInput method)
write_hyper_voxel_to_hdf5() (snudda.detect.detect.SnuddaDetect method)
write_log() (snudda.detect.detect.SnuddaDetect method)
(snudda.detect.prune.SnuddaPrune method)
(snudda.input.input.SnuddaInput method)
(snudda.neurons.neuron_morphology.NeuronMorphology method)
(snudda.place.place.SnuddaPlace method)
(snudda.place.region_mesh.RegionMesh method)
(snudda.utils.benchmark_logging.BenchmarkLogging method)
snudda
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