Created
January 24, 2020 00:21
-
-
Save celoyd/2d7024d264f8fd156fae77e007a42a8f to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# python pca_multiband.py input.jpeg output.tif | |
# n-band image -> PCA -> n-band TIFF image | |
# with lots of hackety assumptions | |
# (e.g., output is same type as input) | |
from sys import argv | |
import rasterio as rio | |
import numpy as np | |
from sklearn import decomposition | |
with rio.open(argv[1]) as src: | |
meta = src.meta | |
pixels = src.read() | |
# pixels[pixels == meta['nodata']] = 0.0 | |
pixels = pixels.astype(np.float32) | |
#pixels = np.nan_to_num(pixels) | |
#pixels[np.isinf(pixels)] = 0.0 | |
dtype = meta["dtype"] | |
count = meta["count"] | |
def normalize(n): | |
m = np.nanmean(n) | |
s = np.nanstd(n) | |
return (n - m) / s | |
# Todo: make this cleaner: | |
pixels = np.dstack([normalize(c).ravel() for c in pixels])[0] | |
pca = decomposition.PCA( | |
n_components=count, whiten=True | |
) | |
pca.fit(pixels) | |
for band in range(len(pca.components_)): | |
weights = ", ".join(["{0:.4g}".format(x) for x in pca.components_[band]]) | |
bidx = band + 1 | |
var = pca.explained_variance_ratio_[band] | |
print(f"Band {bidx} will hold {var:.4g} of variance with weights:\n{weights}") | |
out = pca.transform(pixels) | |
# This is the messy reverse of the messy ravel above: | |
xyz = np.array([out[:, c].reshape(meta["height"], meta["width"]) for c in range(count)]) | |
if dtype == 'uint8': | |
dtype = np.uint16 | |
try: | |
typemax = np.finfo(dtype).max | |
except: | |
typemax = np.iinfo(dtype).max | |
# Scale each band separately to fill out the data type. | |
# (You either really want this or really don't want this.) | |
xyz = np.array([((c - np.amin(c)) / (np.amax(c) - np.amin(c))) * typemax for c in xyz]) | |
xyz = xyz.astype(dtype) | |
meta.update( | |
{ | |
# 'transform': meta['affine'], | |
"driver": "GTiff", | |
"photometric": "none", | |
"dtype": dtype, | |
} | |
) | |
with rio.open(argv[2], "w", **meta) as dst: | |
dst.write(xyz) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment