"""
Generate synthetic n-dimensional spiral datasets for multi-class classification.
This module creates multiple configurations of high-dimensional spiral datasets
with varying sample sizes, noise levels, and dimensionality, useful for testing
machine learning algorithms on complex non-linearly separable patterns.
"""
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import itertools
import json
import os
[docs]
def make_spirals(n_samples=5000, n_classes=2, noise=0.3, dim=3):
"""
Generate an n-dimensional dataset of intertwined spirals.
Creates spiral patterns in n-dimensional space where each class forms
a distinct spiral arm. Supports dimensions 3, 6, 9, and 12.
Parameters
----------
n_samples : int, default=5000
Total number of samples to generate.
n_classes : int, default=2
Number of spiral arms (classes).
noise : float, default=0.3
Standard deviation of Gaussian noise added to each dimension.
dim : int, default=3
Dimensionality of the output space (must be 3, 6, 9, or 12).
Returns
-------
X : ndarray of shape (n_samples, dim)
Generated spiral data points.
y : ndarray of shape (n_samples,)
Class labels for each sample.
"""
X = []
y = []
for i in range(n_classes):
t = np.linspace(0, 4 * np.pi, n_samples // n_classes)
x = t * np.cos(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
y_ = t * np.sin(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
z = t + np.random.normal(0, noise, n_samples // n_classes)
if dim==3:
X.append(np.column_stack([x, y_, z])) # any new dimensions need to be added to this list
# to add more dimensions, apparently you would just keep adding 't' variable from above, to each new dimension,
# as seen below. The question is, how can we iteratively do this while maintaining the binary classification
# that this for loop is creating?
# nesting a loop iterating over the number of dimensions doesn't really work from what I'm seeing. so far
# However, manually adding repeats of the same 3Ds, does work, as seen below -- is this correct?
# for j in range(dim-3): # for anything above the first 3D
if dim==6:
new_d1 = t * np.cos(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d2 = t * np.sin(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d3 = t + np.random.normal(0, noise, n_samples // n_classes)
X.append(np.column_stack([x, y_, z, new_d1, new_d2, new_d3])) # any new dimensions need to be added to this list
if dim==9:
new_d1 = t * np.cos(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d2 = t * np.sin(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d3 = t + np.random.normal(0, noise, n_samples // n_classes)
new_d4 = t * np.cos(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d5 = t * np.sin(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d6 = t + np.random.normal(0, noise, n_samples // n_classes)
X.append(np.column_stack([x, y_, z, new_d1, new_d2, new_d3, new_d4, new_d5, new_d6])) # any new dimensions need to be added to this list
if dim==12:
new_d1 = t * np.cos(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d2 = t * np.sin(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d3 = t + np.random.normal(0, noise, n_samples // n_classes)
new_d4 = t * np.cos(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d5 = t * np.sin(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d6 = t + np.random.normal(0, noise, n_samples // n_classes)
new_d7 = t * np.cos(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d8 = t * np.sin(t + i * np.pi) + np.random.normal(0, noise, n_samples // n_classes)
new_d9 = t + np.random.normal(0, noise, n_samples // n_classes)
X.append(np.column_stack([x, y_, z, new_d1, new_d2, new_d3, new_d4, new_d5, new_d6, new_d7, new_d8, new_d9]))
y.extend([i] * (n_samples // n_classes))
return np.vstack(X), np.array(y)
# parameters to vary across the configurations
N_SAMPLES = list(range(100, 300, 50))
N_CLASSES = [2]
NOISE = [0.3, 0.6, 0.9]
DIM = [3, 6, 9, 12]
[docs]
def generate_spirals_datasets(
n_s=N_SAMPLES,
n_c=N_CLASSES,
n_n=NOISE,
n_d=DIM,
save_path=None,
random_state=42,
):
"""
Generate multiple n-dimensional spiral datasets with varying parameters.
Creates a series of high-dimensional datasets where samples form intertwined
spiral patterns, providing challenging non-linearly separable multi-class
classification problems. Each configuration varies the number of samples,
classes, noise level, and dimensionality.
Parameters
----------
n_s : list of int, default=range(100, 300, 50)
List of sample sizes to generate for each configuration.
n_c : list of int, default=[2]
List of class counts (number of spiral arms).
n_n : list of float, default=[0.3, 0.6, 0.9]
List of noise standard deviations to apply to the data.
n_d : list of int, default=[3, 6, 9, 12]
List of dimensionalities (must be 3, 6, 9, or 12).
save_path : str, optional
Directory path where datasets and configuration files will be saved.
random_state : int, default=42
Random seed for reproducibility.
Returns
-------
None
Saves CSV files for each dataset configuration and a JSON file with
all configuration parameters.
Notes
-----
- Each dataset is saved as 'spirals_data-{i}.csv' where i is the configuration number
- Configuration parameters are saved in 'dataset_config.json'
- The last column 'class' contains class labels
- Spiral patterns become increasingly complex in higher dimensions
Examples
--------
>>> from qbiocode.data_generation import generate_spirals_datasets
>>> generate_spirals_datasets(n_s=[200], n_c=[2], n_n=[0.3], n_d=[3], save_path='data')
Generating spirals dataset...
"""
print("Generating spirals dataset...")
np.random.seed(random_state)
if save_path is None:
save_path = 'spirals_data'
if not os.path.exists(save_path):
os.makedirs(save_path)
# enumerate all possible combinations of parameters based on ranges above
configurations = list(itertools.product(*[n_s, n_c, n_n, n_d]))
# print(configurations)
# print(len(configurations))
count_configs = 1
dataset_config = {}
# populate all the configs with the corresponding argument values
for n_s, n_c, n_n, n_d in configurations:
config = "samples={}, classes={}, noise={}, dimensions={}".format(
n_s, n_c, n_n, n_d
)
# print(count_configs)
X, y = make_spirals(
n_samples=n_s,
n_classes=n_c,
noise=n_n,
dim=n_d
)
# print("Configuration {}/{}: {}".format(count_configs, len(configurations), config))
dataset = pd.DataFrame(X)
dataset['class'] = y
with open( os.path.join( save_path, 'dataset_config.json' ), 'w') as outfile:
dataset_config.update({'spirals_data-{}.csv'.format(count_configs):
{'n_samples': n_s,
'noise': n_n,
'dimensions': n_d
}})
json.dump(dataset_config, outfile, indent=4)
new_dataset = dataset.to_csv( os.path.join( save_path, 'spirals_data-{}.csv'.format(count_configs)), index=False)
count_configs += 1
# plot the last 3 dimensions in each case
# fig = plt.figure()
# ax = fig.add_subplot(111, projection='3d')
# ax.scatter(X[:, n_d-3], X[:, n_d-2],X[:, n_d-1], c=y, cmap='viridis')
# plt.savefig('spirals_data/spirals_data-{}.png'.format(count_configs))
#print(X.shape)
#print(y.shape)
return
