gemseo / third_party

sompy module

Self Organizing Maps

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

Bases: object

name and data, neigh== Bubble or Guassian

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

  • method –

    Default value = ‘Kmeans’)

    By default it is set to Kmeans.

  • n_clusters –

    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 –

    (Default value = 5)

    By default it is set to 5.

hit_map(data=None)[source]
Parameters

data –

Default value = None)

By default it is set to None.

hit_map_cluster_number(data=None)[source]
Parameters

data –

Default value = None)

By default it is set to None.

ind_to_xy(bm_ind)[source]
Parameters

bm_ind –

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

‘uniform’

Parameters

  • data – param wt: (Default value = ‘distance’)

  • Target –

    Default value = None)

    By default it is set to None.

  • wt –

    (Default value = ‘distance’)

    By default it is set to distance.

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

  • x – param y:

  • njb –

    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 –

    Default value = ‘distance’)

    By default it is set to distance.

  • K –

    (Default value = 5)

    By default it is set to 5.

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

  • data – param Target:

  • K –

    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 –

    Default value = 5)

    By default it is set to 5.

  • wt –

    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 –

    Default value = ‘pca’)

    By default it is set to pca.

  • algtype –

    Default value = ‘batch’)

    By default it is set to batch.

  • neighborhoodmethod –

    Default value = ‘gaussian’)

    By default it is set to gaussian.

  • alfatype –

    Default value = ‘inv’)

    By default it is set to inv.

  • alfaini –

    Default value = .5)

    By default it is set to 0.5.

  • alfafinal –

    Default value = .005)

    By default it is set to 0.005.

set_data_labels(dlabel=None)[source]
Parameters

dlabel –

Default value = None)

By default it is set to 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 –

    Default value = None)

    By default it is set to None.

  • mapshape –

    Default value = ‘planar’)

    By default it is set to planar.

  • lattice –

    Default value = ‘rect’)

    By default it is set to rect.

  • mask –

    Default value = None)

    By default it is set to None.

  • compname –

    Default value = None)

    By default it is set to None.

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

  • trainlen –

    Default value = None)

    By default it is set to None.

  • n_job –

    Default value = 1)

    By default it is set to 1.

  • shared_memory –

    Default value = ‘no’)

    By default it is set to no.

  • verbose –

    Default value = ‘on’)

    By default it is set to on.

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

  • training_data – param bmu:

  • H – param radius:

  • bmu –

  • radius –

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 –

    Default value = ‘codebook’)

    By default it is set to codebook.

  • which_dim –

    Default value = ‘all’)

    By default it is set to all.

  • pack –

    Default value = ‘Yes’)

    By default it is set to Yes.

  • text_size –

    Default value = 2.8)

    By default it is set to 2.8.

  • save –

    Default value = ‘No’)

    By default it is set to No.

  • save_dir –

    Default value = ‘empty’)

    By default it is set to empty.

  • grid –

    Default value = ‘No’)

    By default it is set to No.

  • text –

    Default value = ‘Yes’)

    By default it is set to Yes.

  • cmap –

    Default value = ‘None’)

    By default it is set to None.

  • COL_SiZe –

    Default value = 6)

    By default it is set to 6.

gemseo.third_party.sompy.batchtrain(self, njob=1, phase=None, shared_memory='no', verbose='on')[source]
Parameters

  • njob –

    Default value = 1)

    By default it is set to 1.

  • phase –

    Default value = None)

    By default it is set to None.

  • shared_memory –

    Default value = ‘no’)

    By default it is set to no.

  • verbose –

    Default value = ‘on’)

    By default it is set to on.

gemseo.third_party.sompy.chunk_based_bmu_find(self, x, y, y_2)[source]
Parameters

  • x – param y:

  • y_2 –

  • y –

gemseo.third_party.sompy.denormalize_by(data_by, n_vect, n_method='var')[source]
Parameters

  • data_by – param n_vect:

  • n_method –

    Default value = ‘var’)

    By default it is set to var.

  • n_vect –

gemseo.third_party.sompy.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 –

gemseo.third_party.sompy.l(a, b)[source]
Parameters

  • a – param b:

  • b –

gemseo.third_party.sompy.lininit(self)[source]
gemseo.third_party.sompy.normalize(data, method='var')[source]
Parameters

  • data – param method: (Default value = ‘var’)

  • method –

    (Default value = ‘var’)

    By default it is set to var.

gemseo.third_party.sompy.normalize_by(data_raw, data, method='var')[source]
Parameters

  • data_raw – param data:

  • method –

    Default value = ‘var’)

    By default it is set to var.

  • data –

gemseo.third_party.sompy.rect_dist(self, bmu)[source]
Parameters

bmu –

gemseo.third_party.sompy.view_1d(self, text_size, which_dim='all', what='codebook')[source]
Parameters

  • text_size – param which_dim: (Default value = ‘all’)

  • what –

    Default value = ‘codebook’)

    By default it is set to codebook.

  • which_dim –

    (Default value = ‘all’)

    By default it is set to all.

gemseo.third_party.sompy.view_2d(self, text_size, which_dim='all', what='codebook')[source]
Parameters

  • text_size – param which_dim: (Default value = ‘all’)

  • what –

    Default value = ‘codebook’)

    By default it is set to codebook.

  • which_dim –

    (Default value = ‘all’)

    By default it is set to all.

gemseo.third_party.sompy.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 – param which_dim: (Default value = ‘all’)

  • what –

    Default value = ‘codebook’)

    By default it is set to codebook.

  • save –

    Default value = ‘No’)

    By default it is set to No.

  • grid –

    Default value = ‘Yes’)

    By default it is set to Yes.

  • save_dir –

    Default value = ‘empty’)

    By default it is set to empty.

  • text –

    Default value = ‘Yes’)

    By default it is set to Yes.

  • CMAP –

    Default value = ‘None’)

    By default it is set to None.

  • col_sz –

    Default value = None)

    By default it is set to None.

  • which_dim –

    (Default value = ‘all’)

    By default it is set to all.