gemseo.third_party.sompy module#

Self Organizing Maps#

class SOM(name, Data, mapsize=None, norm_method='var', initmethod='pca', neigh='Guassian')[source]#

Bases: object

name and data, neigh== Bubble or Guassian

Parameters:

name (str)
mapsize (int | None)
norm_method (str) --

By default it is set to "var".
initmethod (str) --

By default it is set to "pca".
neigh (str) --

By default it is set to "Guassian".

calc_map_dist()[source]#

Return type:: None

cluster(method='Kmeans', n_clusters=8)[source]#

Parameters:

method (str) --
Default value = 'Kmeans')

By default it is set to "Kmeans".
n_clusters (int) --
Default value = 8)

By default it is set to 8.

find_K_nodes(data, K=5)[source]#

Parameters:

data -- param K: (Default value = 5)
K (int) --
(Default value = 5)

By default it is set to 5.

hit_map(data=None)[source]#

Parameters:: data -- Default value = None)
Return type:: None

hit_map_cluster_number(data=None)[source]#

Parameters:: data -- Default value = None)

ind_to_xy(bm_ind)[source]#

Parameters:: bm_ind

init_map()[source]#

Return type:: None

node_Activation(data, wt='distance', Target=None)[source]#

‘uniform’

Parameters:

data -- param wt: (Default value = 'distance')
Target -- Default value = None)
wt (str) --
(Default value = 'distance')

By default it is set to "distance".

para_bmu_find(x, y, njb=1)[source]#

Parameters:

x -- param y:
njb (int) --
Default value = 1)

By default it is set to 1.
y

predict(X_test, K=5, wt='distance')[source]#

‘uniform’

Parameters:

X_test -- param K: (Default value = 5)
wt (str) --
Default value = 'distance')

By default it is set to "distance".
K (int) --
(Default value = 5)

By default it is set to 5.

predict_Probability(data, Target, K=5)[source]#

Parameters:

data -- param Target:
K (int) --
Default value = 5)

By default it is set to 5.
Target

predict_by(data, Target, K=5, wt='distance')[source]#

‘uniform’

Parameters:

data -- param Target:
K (int) --
Default value = 5)

By default it is set to 5.
wt (str) --
Default value = 'distance')

By default it is set to "distance".
Target

project_data(data)[source]#

Parameters:: data

set_algorithm(initmethod='pca', algtype='batch', neighborhoodmethod='gaussian', alfatype='inv', alfaini=0.5, alfafinal=0.005)[source]#

initmethod = ['random', 'pca'] algos = ['seq','batch'] all_neigh = ['gaussian','manhatan','bubble','cut_gaussian','epanechicov' ] alfa_types = ['linear','inv','power']

Parameters:

initmethod (str) --
Default value = 'pca')

By default it is set to "pca".
algtype (str) --
Default value = 'batch')

By default it is set to "batch".
neighborhoodmethod (str) --
Default value = 'gaussian')

By default it is set to "gaussian".
alfatype (str) --
Default value = 'inv')

By default it is set to "inv".
alfaini (float) --
Default value = .5)

By default it is set to 0.5.
alfafinal (float) --
Default value = .005)

By default it is set to 0.005.

Return type:

None

set_data_labels(dlabel=None)[source]#

Parameters:: dlabel (str | None) -- Default value = None)
Return type:: None

set_topology(mapsize=None, mapshape='planar', lattice='rect', mask=None, compname=None)[source]#

all_mapshapes = ['planar','toroid','cylinder'] all_lattices = ['hexa','rect']

Parameters:

mapsize (int | None) -- Default value = None)
mapshape (str) --
Default value = 'planar')

By default it is set to "planar".
lattice (str) --
Default value = 'rect')

By default it is set to "rect".
mask -- Default value = None)
compname (str | None) -- Default value = None)

Return type:

None

train(trainlen=None, n_job=1, shared_memory='no', verbose='on')[source]#

Parameters:

trainlen -- Default value = None)
n_job (int) --
Default value = 1)

By default it is set to 1.
shared_memory (str) --
Default value = 'no')

By default it is set to "no".
verbose (str) --
Default value = 'on')

By default it is set to "on".

Return type:

None

update_codebook_voronoi(training_data, bmu, H, radius)[source]#

Parameters:

training_data -- param bmu:
H -- param radius:
bmu
radius (float)

view_map(what='codebook', which_dim='all', pack='Yes', text_size=2.8, save='No', save_dir='empty', grid='No', text='Yes', cmap='None', COL_SiZe=6)[source]#

Parameters:

what (str) --
Default value = 'codebook')

By default it is set to "codebook".
which_dim (str) --
Default value = 'all')

By default it is set to "all".
pack (str) --
Default value = 'Yes')

By default it is set to "Yes".
text_size (float) --
Default value = 2.8)

By default it is set to 2.8.
save (str) --
Default value = 'No')

By default it is set to "No".
save_dir (str) --
Default value = 'empty')

By default it is set to "empty".
grid (str) --
Default value = 'No')

By default it is set to "No".
text (str) --
Default value = 'Yes')

By default it is set to "Yes".
cmap (str) --
Default value = 'None')

By default it is set to "None".
COL_SiZe (int) --
Default value = 6)

By default it is set to 6.

Return type:

None

batchtrain(self, njob=1, phase=None, shared_memory='no', verbose='on')[source]#

Parameters:

njob (int) --
Default value = 1)

By default it is set to 1.
phase -- Default value = None)
shared_memory (str) --
Default value = 'no')

By default it is set to "no".
verbose (str) --
Default value = 'on')

By default it is set to "on".

Return type:

None

chunk_based_bmu_find(self, x, y, y_2)[source]#

Parameters:

x -- param y:
y_2
y

denormalize_by(data_by, n_vect, n_method='var')[source]#

Parameters:

data_by -- param n_vect:
n_method (str) --
Default value = 'var')

By default it is set to "var".
n_vect

grid_dist(self, bmu_ind)[source]#

som and bmu_ind depending on the lattice "hexa" or "rect" we have different grid distance functions. bmu_ind is a number between 0 and number of nodes-1. depending on the map size bmu_coord will be calculated and then distance matrix in the map will be returned

Parameters:: bmu_ind

l(a, b)[source]#

Parameters:

a -- param b:
b

lininit(self)[source]#

normalize(data, method='var')[source]#

Parameters:

data -- param method: (Default value = 'var')
method (str) --
(Default value = 'var')

By default it is set to "var".

normalize_by(data_raw, data, method='var')[source]#

Parameters:

data_raw -- param data:
method (str) --
Default value = 'var')

By default it is set to "var".
data

rect_dist(self, bmu)[source]#

Parameters:: bmu

view_1d(self, text_size, which_dim='all', what='codebook')[source]#

Parameters:

text_size (int) -- param which_dim: (Default value = 'all')
what (str) --
Default value = 'codebook')

By default it is set to "codebook".
which_dim (str) --
(Default value = 'all')

By default it is set to "all".

Return type:

None

view_2d(self, text_size, which_dim='all', what='codebook')[source]#

Parameters:

text_size (int) -- param which_dim: (Default value = 'all')
what (str) --
Default value = 'codebook')

By default it is set to "codebook".
which_dim (str) --
(Default value = 'all')

By default it is set to "all".

Return type:

None

view_2d_Pack(self, text_size, which_dim='all', what='codebook', save='No', grid='Yes', save_dir='empty', text='Yes', CMAP='None', col_sz=None)[source]#

Parameters:

text_size (int) -- param which_dim: (Default value = 'all')
what (str) --
Default value = 'codebook')

By default it is set to "codebook".
save (str) --
Default value = 'No')

By default it is set to "No".
grid (str) --
Default value = 'Yes')

By default it is set to "Yes".
save_dir (str) --
Default value = 'empty')

By default it is set to "empty".
text (str) --
Default value = 'Yes')

By default it is set to "Yes".
CMAP (str) --
Default value = 'None')

By default it is set to "None".
col_sz -- Default value = None)
which_dim (str) --
(Default value = 'all')

By default it is set to "all".

Return type:

None