bridgescaler 0.8.3

Tool to automagically save scikit-learn scaler properties to a portable, readable format.

bridgescaler

Bridge your scikit-learn-style scaler parameters between Python sessions and users. Bridgescaler allows you to save the properties of a scikit-learn-style scaler object to a json file, and then repopulate a new scaler object with the same properties.

Dependencies

• scikit-learn
• numpy
• pandas
• xarray
• pytdigest

Installation

For a stable version of bridgescaler, you can install from PyPI.

pip install bridgescaler

For the latest version of bridgescaler, install from github.

git clone https://github.com/NCAR/bridgescaler.git
cd bridgescaler
pip install .

Usage

bridgescaler supports all the common scikit-learn scaler classes:

• StandardScaler
• RobustScaler
• MinMaxScaler
• MaxAbsScaler
• QuantileTransformer
• PowerTransformer
• SplineTransformer

First, create some synthetic data to transform.

import numpy as np
import pandas as pd

# specify distribution parameters for each variable
locs = np.array([0, 5, -2, 350.5], dtype=np.float32)
scales = np.array([1.0, 10, 0.1, 5000.0])
names = ["A", "B", "C", "D"]
num_examples = 205
x_data_dict = {}
for l in range(locs.shape[0]):
    # sample from random normal with different parameters
    x_data_dict[names[l]] = np.random.normal(loc=locs[l], scale=scales[l], size=num_examples)
x_data = pd.DataFrame(x_data_dict)

Now, let's fit and transform the data with StandardScaler.

from sklearn.preprocessing import StandardScaler
from bridgescaler import save_scaler, load_scaler

scaler = StandardScaler()
scaler.fit_transform(x_data)
filename = "x_standard_scaler.json"
# save to json file
save_scaler(scaler, filename)

# create new StandardScaler from json file information.
new_scaler = load_scaler(filename) # new_scaler is a StandardScaler object

Distributed Scaler

The distributed scalers allow you to calculate scaling parameters on different subsets of a dataset and then combine the scaling factors together to get representative scaling values for the full dataset. Distributed Standard Scalers, MinMax Scalers, and Quantile Transformers have been implemented and work with both tabular and muliti-dimensional patch data in numpy, pandas DataFrame, and xarray DataArray formats. By default, the scaler assumes your channel/variable dimension is the last dimension, but if channels_last=False is set in the __init__, transform, or inverse_transform methods, then the 2nd dimension is assumed to be the variable dimension. It is possible to fit data with one ordering and then transform it with a different one.

For large datasets, it may be expensive to redo the scalers if you want to use a subset or different ordering of variables. However, in bridgescaler, the Distributed Scalers all support arbitrary ordering and subsets of variables for transforms if the input data are in a Xarray DataArray or Pandas DataFrame with variable names that match the original data.

Example:

from bridgescaler.distributed import DStandardScaler
import numpy as np

x_1 = np.random.normal(0, 2.2, (20, 5, 4, 8))
x_2 = np.random.normal(1, 3.5, (25, 4, 8, 5))

dss_1 = DStandardScaler(channels_last=False)
dss_2 = DStandardScaler(channels_last=True)
dss_1.fit(x_1)
dss_2.fit(x_2)
dss_combined = np.sum([dss_1, dss_2])

dss_combined.transform(x_1, channels_last=False)

Group Scaler

The group scalers use the same scaling parameters for a group of similar variables rather than scaling each column independently. This is useful for situations where variables are related, such as temperatures at different height levels.

Groups are specified as a list of column ids, which can be column names for pandas dataframes or column indices for numpy arrays.

For example:

from bridgescaler.group import GroupStandardScaler
import pandas as pd
import numpy as np
x_rand = np.random.random(size=(100, 5))
data = pd.DataFrame(data=x_rand, 
                    columns=["a", "b", "c", "d", "e"])
groups = [["a", "b"], ["c", "d"], "e"]
group_scaler = GroupStandardScaler()
x_transformed = group_scaler.fit_transform(data, groups=groups)

"a" and "b" are a single group and all values of both will be included when calculating the mean and standard deviation for that group.

Deep Scaler

The deep scalers are designed to scale 2 or 3-dimensional fields input into a deep learning model such as a convolutional neural network. The scalers assume that the last dimension is the channel/variable dimension and scales the values accordingly. The scalers can support 2D or 3D patches with no change in code structure. Support is provided for DeepStandardScaler and DeepQuantileTransformer.

Example:

from bridgescaler.deep import DeepStandardScaler
import numpy as np
np.random.seed(352680)
n_ex = 5000
n_channels = 4
dim = 32
means = np.array([1, 5, -4, 2.5], dtype=np.float32)
sds = np.array([10, 2, 43.4, 32.], dtype=np.float32)
x = np.zeros((n_ex, dim, dim, n_channels), dtype=np.float32)
for chan in range(n_channels):
    x[..., chan] = np.random.normal(means[chan], sds[chan], (n_ex, dim, dim))
dss = DeepStandardScaler()
dss.fit(x)
x_transformed = dss.transform(x)