# Principal component analysis for multi-spectral data ¶

## Background¶

Principal Component Analysis (PCA) is a popular technique for dimensionality reduction. It can be used to explore patterns in high-dimensional data and assist unsupervised learning.

Principal components are a series of linear combinations of the original variables, among which the first principal component accounts for the greatest variance within a dataset. Each subsequent principal component accounts for the next greatest possible variance and is uncorrelated with the previously defined components.

This technique is useful for understanding Sentinel-2 data as images are captured in 12 spectral bands but only 3 variables can be visualized in a RGB composite. PCA can also be applied to timeseries data to investigate temporal evolution patterns for different land cover types.

## Description¶

This notebook demonstrates a principal component analysis for Sentinel-2 multi-spectal data. Following steps are covered:

2. Applying PCA to transform and visualize data.

## Getting started¶

To run this analysis, run all the cells in the notebook, starting with the “Load packages” cell.

Import Python packages that are used for the analysis.

[1]:

%matplotlib inline

import datacube
from sklearn.decomposition import PCA

import sys
sys.path.append('../Scripts')
from dea_plotting import rgb
from dea_classificationtools import sklearn_flatten, sklearn_unflatten

/env/lib/python3.6/site-packages/datacube/storage/masking.py:4: DeprecationWarning: datacube.storage.masking has moved to datacube.utils.masking
category=DeprecationWarning)


### Connect to the datacube¶

Connect to the datacube so we can access DEA data.

[2]:

dc = datacube.Datacube(app='Principal_component_analysis')


### Analysis parameters¶

This section defines the analysis parameters, including

• lat, lon: center lat/lon for the area of interest

• buffer: the indow size around the centre lat/lon for the area of interest

• time_range: time period to be investigated

• min_gooddata: minimumum fraction of good-data in the image before it while be returned

• bands: spectral bands to be explored

The default location is the Norman River, Qld.

To limit overall memory usage, if a larger analysis window or higher resolution is desired, the time period should be reduced accordingly.

[3]:

lat, lon = -17.5687, 140.9653
buffer = 0.075
time_range = ('2019-12', '2020-03')
bands = [
'nbar_blue', 'nbar_green', 'nbar_red', 'nbar_red_edge_1', 'nbar_red_edge_2',
'nbar_red_edge_3', 'nbar_nir_2', 'nbar_swir_2', 'nbar_swir_3'
]
min_gooddata = 0.9


[4]:

# Define the query dict
query = {
'time': time_range,
'x': (lon - buffer, lon + buffer),
'y': (lat + buffer, lat - buffer),
'output_crs': 'epsg:3577',
'resolution': (-10, 10),
'group_by': 'solar_day',
'measurements': bands
}

[5]:

# Load the data
products=['s2a_ard_granule', 's2b_ard_granule'],
min_gooddata=min_gooddata,
**query)

Finding datasets
s2a_ard_granule
s2b_ard_granule
Counting good quality pixels for each time step
Filtering to 3 out of 8 time steps with at least 90.0% good quality pixels

[6]:

# Visualize data using selected input spectral bands
rgb(ds,
bands=['nbar_swir_2', 'nbar_nir_2', 'nbar_red_edge_1'],
col='time',
col_wrap=3)


## Applying PCA to transform and visualize data¶

To perform a PCA, data is first transformed into a numpy array that can be used by sklearn using the DEA function sklearn_flatten.

[7]:

x = sklearn_flatten(ds)


A PCA model is generated with 3 principal components and fitted on the data.

[8]:

pca = PCA(n_components=3)
pca.fit(x)

[8]:

PCA(n_components=3)


We can investigate how much variance is accounted for in each principal component. In the default example, the first principal component accounts for a much high variance than the next two.

This step can help determine whether more principal components are needed.

[9]:

print('Relative variance in principal components:',
pca.explained_variance_ratio_)

Relative variance in principal components: [0.84617012 0.09495869 0.05051923]


The input data can now be transformed into this new reference space and rearranged into an xarray.Dataset compatible with our input data.

[10]:

predict = pca.transform(x)

[11]:

out = sklearn_unflatten(predict, ds)
out = out.to_dataset(dim=out.dims[0]).transpose('time', 'y', 'x')


### Visualise PCA results¶

[12]:

# Plot PCA bands
rgb(out,
bands=[2, 1, 0],
col='time',
col_wrap=3,
percentile_stretch=[0.08, 0.92])


Contact: If you need assistance, please post a question on the Open Data Cube Slack channel or on the GIS Stack Exchange using the open-data-cube tag (you can view previously asked questions here). If you would like to report an issue with this notebook, you can file one on Github.

Compatible datacube version:

[13]:

print(datacube.__version__)

1.8.3


## Tags¶

Browse all available tags on the DEA User Guide’s Tags Index

Tags: sandbox compatible, NCI compatible, sentinel 2, dea_datahandling, dea_classificationtools, dea_plotting, rgb, sklearn_flatten, sklearn_unflatten, principal component analysis, statistics