I tried to make an algorithm in Python where I entered a georeferenced raster (EPSG 32722 projection system), all its NaN values ​​were transformed to zero, and then a new image was saved with the EPSG 4326 projection system.

import skimage.io
import pandas as pd
import numpy as np
from sklearn.impute import SimpleImputer

pathhr = 'C:\\Users\\dataset\\S30W051.tif'
HR = skimage.io.imread(pathhr)
df1 = pd.DataFrame(HR)
imputer = SimpleImputer(fill_value=np.nan, strategy='mean')
X = imputer.fit_transform(df1)
X = pd.DataFrame(X, columns=df1.columns)

#save function
savedata = df1.to_numpy()
skimage.io.imsave('C:\\Users\\dataset\\S30W051_TEST.tif', savedata)

But when I save my raster at the end of this script, I get a non-georeferenced TIFF raster.

How do I save this new raster with the EPSG 4326 projection system?

  • 3
    Use a geospatial library as rasterio instead of skimage
    – gene
    Jun 5 '21 at 15:25

It's easy using a library that's designed to handle georeferenced raster data like GDAL or rasterio (based on GDAL).

Here is an example based on the docs for reprojecting with rasterio:

import numpy as np
import rasterio as rio
from rasterio.warp import calculate_default_transform, reproject, Resampling
from sklearn.impute import SimpleImputer

pathhr = 'C:\\Users\\dataset\\S30W051.tif'
pathout = 'C:\\Users\\dataset\\S30W051_TEST.tif'

dst_crs = 'EPSG:4326'
imputer = SimpleImputer(fill_value=np.nan, strategy='mean')

with rio.open(pathhr) as src:
    profile = src.profile.copy()
    transform, width, height = calculate_default_transform(
        src.crs, dst_crs, src.width, src.height, *src.bounds)
        'crs': dst_crs,
        'transform': transform,
        'width': width,
        'height': height

    with rio.open(pathout, 'w', **profile) as dst:
        for i in range(1, src.count + 1):

            data = np.nan_to_num(src.read(i))
            data = imputer.fit_transform(data)  # use array not pandas df 

                source=rio.band(src, i),
                destination=rio.band(dst, i),

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